From rotor@cmr.uq.edu.au Sun Aug 1 20:48:04 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Sun Aug 1 19:48:04 2004 Subject: [MINC-users] minc output problem In-Reply-To: References: Message-ID: On Mon, 26 Jul 2004, Peter SAVADIJIEV wrote: > When I attempt to write my output minc files to disk I get an error. I tried > different things, thinking that it may be a problem with my program, but to no > avail. > > I kept the code exactly the same, and I used one of the > mnc files that I have as input. I still got exactly the same > error, which makes me believe that it's not a problem with the code as > such. > > The error message reads: > nccreate: Bad Flag > micreate: MINC package entry point > Error: opening MINC file "output.mnc". Peter, I'm at somewhat of a loss with respects to this error. Can you run any of the executables that are included in the core minc package? (mincmath, mincinfo, etc?) Are you sure you have write permission to the output directory? -- Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From haytham@umich.edu Fri Aug 6 11:51:03 2004 From: haytham@umich.edu (haytham@umich.edu) Date: Fri Aug 6 10:51:03 2004 Subject: [MINC-users] ANIMAL Message-ID: <1091803846.41139ac6de137@mail.umich.edu> This is a message I sent earlier but did not get any responses. Please help: I am trying to follow the procedure to automatically segment and label the volume that is described in Dr. Collins paper titled "ANIMAL+INSECT: Improved Cortical Structure Segmentation." I was able to do the following steps: 1. Linear Registration (MRI to Stereotaxic Space) (mritotal) 2. Image Intensity Non-Uniformity Correction (N3 Package) 3. Nonlinear Registration With Average Brain Target (with nlfit/animal) 4. Identify Grey Matter, White Matter and CSF Voxels (classify package) The last step (5) of the procedure is to take the output of the linear and non-linear registration and combine the classified data to achieve a segmentation. Ok, I know stx_segment accomplishes this last crutial step. Where is this script located? I downloaded and installed all the software avaialble from http://www.bic.mni.mcgill.ca/software/distribution/ and I can not find the script. I am trying to validate some of the results mentioned in this published paper. On more thing that I dont understand: Animal stands for Automatic Nonlinear Image Matching and Anatomical Labeling. The animal package that is available to download (to my knowledge) includes only the "Automatic Nonlinear Image Matching" part. Where are the "Anatomical Labeling" routines? Can someone HELP me please? Thanks in advance -haytham From stever@bic.mni.mcgill.ca Sun Aug 8 13:39:04 2004 From: stever@bic.mni.mcgill.ca (Steve ROBBINS) Date: Sun Aug 8 12:39:04 2004 Subject: [MINC-users] ANIMAL In-Reply-To: <1091803846.41139ac6de137@mail.umich.edu>; from haytham@umich.edu on Fri, Aug 06, 2004 at 10:50:46AM -0400 References: <1091803846.41139ac6de137@mail.umich.edu> Message-ID: <20040808123823.B18215538@shadow.bic.mni.mcgill.ca> On Fri, Aug 06, 2004 at 10:50:46AM -0400, haytham@umich.edu wrote: > This is a message I sent earlier but did not get any responses. Please help: > > I am trying to follow the procedure to automatically segment and label the > volume that is described in Dr. Collins paper titled "ANIMAL+INSECT: Improved > Cortical Structure Segmentation." I was able to do the following steps: > > 1. Linear Registration (MRI to Stereotaxic Space) (mritotal) > 2. Image Intensity Non-Uniformity Correction (N3 Package) > 3. Nonlinear Registration With Average Brain Target (with nlfit/animal) > 4. Identify Grey Matter, White Matter and CSF Voxels (classify package) > > The last step (5) of the procedure is to take the output of the linear and > non-linear registration and combine the classified data to achieve a > segmentation. Ok, I know stx_segment accomplishes this last crutial step. Where > is this script located? I downloaded and installed all the software avaialble > from http://www.bic.mni.mcgill.ca/software/distribution/ and I can not find the > script. I believe that you need to contact L.Collins directly for it. > On more thing that I dont understand: > Animal stands for Automatic Nonlinear Image Matching and Anatomical Labeling. > The animal package that is available to download (to my knowledge) includes > only the "Automatic Nonlinear Image Matching" part. Where are the "Anatomical > Labeling" routines? That is what "stx_segment" does. -Steve From tosa@nmr.mgh.harvard.edu Tue Aug 10 17:24:04 2004 From: tosa@nmr.mgh.harvard.edu (Yasunari Tosa) Date: Tue Aug 10 16:24:04 2004 Subject: [MINC-users] mni_autoreg-0.98r fails 3 tests Message-ID: <41192EDB.7050703@nmr.mgh.harvard.edu> Hi, mni_autoreg-0.98r : "make check" fails 3 tests. Is this "normal"? Can you tell me how I can fix the problem? I'm running this on Dual PIII (1 Ghz and 1 Gbyte memory). PASS: linear-1 PASS: linear-2 PASS: linear-3 PASS: nonlinear-2 PASS: nonlinear-3 PASS: nonlinear-4 PASS: nonlinear-5 FAIL: nonlinear-6 FAIL: nonlinear-7 FAIL: nonlinear-8 I build the tool with CFLAGS="-g -O2". My other minc tool versions are minc-1.2. EBTKS-1.3, netcdf-3.51, N3-1.09. Thank you. Tosa -- Yasunari Tosa, Ph.D. Email: tosa@nmr.mgh.harvard.edu NMR Ctr, Mass. General Hospital TEL: 617-726-4050 Building 149, 13th Street Charlestown, MA 02129 USA From bert@bic.mni.mcgill.ca Tue Aug 10 18:04:04 2004 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Tue Aug 10 17:04:04 2004 Subject: [MINC-users] Warning re: netCDF 3.5.1 Message-ID: To all MINC users, An incompatibility has just been discovered between all current versions of MINC and netCDF 3.5.1. Until further notice, please do not use netCDF 3.5.1 with MINC 1.2, MINC 2.0.07, or any earlier MINC versions! You can check the version of netCDF installed on your system by typing: ncdump -X The last line of the output will contain the netCDF version number. As of now the IRIX systems at the Brain Imaging Centre should be running netCDF 3.5.0, which is fine. If for some reason you _must_ use netCDF 3.5.1 with MINC, you should edit all copies of minc.h to change the line: #define MI_MAX_IMGDIMS MAX_VAR_DIMS to read: #define MI_MAX_IMGDIMS 100 Rebuild the MINC libraries and all MINC tools after making this change. I will make a new release of MINC 2.0 and 1.0 available on our website, http://www.bic.mni.mcgill.ca/software/minc, as soon as possible, hopefully within the week. Please contact me if you would like any further information. -bert From rotor@cmr.uq.edu.au Tue Aug 10 23:21:04 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Tue Aug 10 22:21:04 2004 Subject: [MINC-users] Test linux binary packages. Message-ID: Some of you out there may be interested in testing some debian (deb) and redhat (rpm) packages of most of the MINC toolchain: http://www.bic.mni.mcgill.ca/~rotor/distro/deb http://www.bic.mni.mcgill.ca/~rotor/distro/rpm These were built on a P4. There may be a few errant dependancies that need to be included in these packages. (netpbm for example). The Redhat packages are completely untested (even by me) they just happen to be ouput along with the deb packages as part of the build process. I'd be interested to know if they work for others, and no N3 is not in here, it still needs a bit of work to make it suitable for binary packaging! :) -- Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From tosa@nmr.mgh.harvard.edu Wed Aug 11 14:40:03 2004 From: tosa@nmr.mgh.harvard.edu (Yasunari Tosa) Date: Wed Aug 11 13:40:03 2004 Subject: [MINC-users] mni_autoreg 0.98r problem resolved by switching back to netcdf3.5.0 Message-ID: <411A59D7.6070501@nmr.mgh.harvard.edu> Update of the problem in "mni_autoreg 0.98r make check" failures: I replaced netcdf3.5.1 with netcdf3.5.0 and now all tests pass. Thus until the fixed mni tools, you should use netcdf 3.5.0. Tosa -- Yasunari Tosa, Ph.D. Email: tosa@nmr.mgh.harvard.edu NMR Ctr, Mass. General Hospital TEL: 617-726-4050 Building 149, 13th Street Charlestown, MA 02129 USA From bert@bic.mni.mcgill.ca Thu Aug 12 18:37:04 2004 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Thu Aug 12 17:37:04 2004 Subject: [MINC-users] MINC 1.3 released Message-ID: Hello minc-users, I've placed a new release of MINC, version 1.3, on our usual software distribution sites: http://www.bic.mni.mcgill.ca/software/distribution/ http://www.bic.mni.mcgill.ca/software/minc/ MINC 1.3 fixes the recently discovered incompatibility with netCDF 3.5.1, and fixes one or two other bugs and minor build issues. One potentially serious bug with minccalc has been fixed, it would affect you if you use minccalc with MINC files which contain a vector dimension. A -version flag has been added to most of the tools. See the NEWS and ChangeLog files for additional details. MINC 1.3 has been built successfully on Linux (RedHat) and IRIX. -bert From rgilmore@tulane.edu Sun Aug 15 19:12:04 2004 From: rgilmore@tulane.edu (renee gilmore) Date: Sun Aug 15 18:12:04 2004 Subject: [MINC-users] windows xp and minc Message-ID: <000801c48315$04ed50f0$88d55181@bunny> This is a multi-part message in MIME format. ------=_NextPart_000_0005_01C482EB.1B1D0A70 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I was wondering can minc be installed using windows xp and java. my = computer does not have fortran or c++. I have installed the pre-built = win32 binary but I am not sure how to proceed from here. Thanks Renee Gilmore rgilmore@tulane.edu ------=_NextPart_000_0005_01C482EB.1B1D0A70 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi,
I was wondering can minc be installed = using windows=20 xp and java. my computer does not have fortran or c++.  I = have =20 installed the pre-built win32 binary but I am not sure how to proceed = from here.=20 Thanks
Renee Gilmore
rgilmore@tulane.edu
------=_NextPart_000_0005_01C482EB.1B1D0A70-- From haytham@umich.edu Tue Aug 17 15:41:05 2004 From: haytham@umich.edu (haytham@umich.edu) Date: Tue Aug 17 14:41:05 2004 Subject: [MINC-users] mincmask In-Reply-To: <200408161601.i7GG15Yq19238752@shadow.bic.mni.mcgill.ca> References: <200408161601.i7GG15Yq19238752@shadow.bic.mni.mcgill.ca> Message-ID: <1092768003.412251039529c@mail.umich.edu> Hello everyone, I just have a small question: what package is mincmask part of? I am trying to invert a mask volume and I am wondering if there is a new package or a mincmask itself that can let me do that. Thanks -haytham From sylvain@bic.mni.mcgill.ca Tue Aug 17 17:53:04 2004 From: sylvain@bic.mni.mcgill.ca (Sylvain MILOT) Date: Tue Aug 17 16:53:04 2004 Subject: [MINC-users] mincmask In-Reply-To: <1092768003.412251039529c@mail.umich.edu> Message-ID: Hello, mincmask belongs, as far as I know, in Louis Collins' personal mincstuff and I'm not sure if it ever migrated officially into the minc distribution - just checked and it isn't there. Anyway, you could invert your mask with 'mincmath -not in.mnc out.mnc' Sylvain On Tue, 17 Aug 2004 haytham@umich.edu wrote: > Hello everyone, I just have a small question: > > what package is mincmask part of? > I am trying to invert a mask volume and I am wondering if there is a new package > or a mincmask itself that can let me do that. > Thanks > > -haytham > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain@bic.mni.mcgill.ca) (trinity@bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, 1996 Fax: 8948 Mobile : (514) 712-1768 Office : 527 Pine, room 204 From yves.roy@umontreal.ca Mon Aug 23 17:09:05 2004 From: yves.roy@umontreal.ca (Roy Yves) Date: Mon Aug 23 16:09:05 2004 Subject: [MINC-users] REPRIC - fMRI conferences and workshops Message-ID: The REPRIC is pleased to announce a tutorial/workshop on functional magnetic resonance imaging (fMRI) to take place this fall (late November-early December). The duration of this course will be about one week and different topics will be covered including: * planification and experimental designs * pre-processing and statistical analysis of data * results visualisation * batch mode * SPM and fMRIstat software-methodologies * available ressource for help and support There will be both theoretical presentations and hands-on practical sessions, so that participans can learn both the "how" and the "why" of each step. This workshop is aimed at users of all levels: future, beginners and advanced. In order to set up an event that will be really helpful to everyone, we ask you for your feedback by completing a brief questionnaire. You can do so by using the online form on the REPRIC web site http://www.rsmnq.ca/repric/en/repric_digest_conferences.htm before September 20, 2004. Your suggestions for topics of special interest are welcome. Thanks, the organizers: Pascal Belin, Université de Montréal Jorge Armony, Douglas Hospital, McGill University Coordination of the event by Yves Roy, REPRIC technical coordinator. yves.roy@umontreal.ca repricweb@umontreal.ca From yves.roy@umontreal.ca Tue Aug 24 13:39:03 2004 From: yves.roy@umontreal.ca (Roy Yves) Date: Tue Aug 24 12:39:03 2004 Subject: [MINC-users] fMRIstat event-related questions + error Message-ID: Dear BIC users: I have a question concerning an fMRI event-related study on language processing using fMRIstat. 1) Question on duration of events 2) Error in Matlab ___________________________ 1) The study roughly consists in presenting visual stimuli of strings of characters and the subjects have to answer whether the stumulus was a word of high imageability, low imageability, a non-word, or for a baseline condition, a string of capital or small letters (so 4 conditions/regressors). Amond other things, I am looking for guidelines on how to set the duration (of events) values in the events matrix. for event-related (I know it may depends on the actual experiment and what the neuropsychologist looking for but still, guidelines would be welcome). mouldy 104% * visual stimuli last 200ms, and where, * a subject has to answer as to the nature of the stimulus and where * stimuli belonging to different conditions are separated in time by an ISI (inter-stimulus interval) ranging from 2000ms to 3000ms, and where * the subject is allowed 1500ms after the beginning of the stimulus, how should I go about determining the event duration: a) 0 (default value in fMRIstat) b) 200 ms (duration of the stimulus itself) c) actual subject response time d) ISI Some people I talked to suggested 0 ms, some the ISI, and some told me to be cautions in that choice (pointing to the article by Randy Buckner: Event-Related fMRI and the Hemodynamic Response, HBM 6:373-377(1998). I am looking for values commonly used in similar situations, as well as justification/rationale behind that choice (if you are aware of some interesting papers on the topics as well). 2) Here is the batch I ran: %_________________________________________________________________ % Batch for the definition of the design matrix and parameter estimation % for a single subject, one run. % TR = 3s, % 103 frames per run = 309 seconds/run % frametimes is a row vector in which you enter the time, in seconds % at which each frame was acquired. %______________________________________________________________ % % Q? - The frametimes defined below just uses the known TR set % in the scanner when the experiment was defined. How to ensure % that the frametimes defined like this always corresponds to % the frametimes as found in the minc images? %_______________________________________________________________ frametimes = (0:102) * 3; %_______________________________________________________ % MOSAIC 24 ascending: % Delay between beginning of frame and first slice: 0ms % Time between slices: ~92ms (for 64x64) % Number of slice per volume: 28 % Acquisition: ascending, interleaved :q bullcalf 122% more batch.m %_________________________________________________________________ % % Analysis for subject 5 A-B, run 1 %_________________________________________________________________ % TR = 3s, % 103 frames per run = 309 seconds/run % frametimes is a row vector in which you enter the time, in seconds % at which each frame was acquired. %______________________________________________________________ % % Q? - The frametimes defined below just uses the known TR set % in the scanner when the experiment was defined. How to ensure % that the frametimes defined like this always corresponds to % the frametimes as found in the minc images? %_______________________________________________________________ frametimes = (0:102) * 3; %_______________________________________________________ % MOSAIC 24 ascending: % Delay between beginning of frame and first slice: 0ms % Time between slices: ~92ms (for 64x64) % Number of slice per volume: 28 % Acquisition: ascending, interleaved % (first slice = bottom slice i.e. slice labeled 1 in MINC file so that: % #1___ __W__ % #2___/ \ ^\ | % #3__@ o o @ | \ ^ % :__| u | ^ \ | Ascending, interleaved % #N-1___\ - / | \ ^ % #N____\___/ ^ \| % % slice number: 1 2 ... N-2 N-1 N=28 % slicetimes = [ ... 0.920 1.840 0 ]) % % slicetimes is a row vector of relative slice acquisition times. %_______________________________________________________________ % % Q1? - time relative to the frametimes, i.e. in descending % sequential acquisition, a slice time of 0 for slice #1 % means that the first slice started to be acquired at the % same time the frame started to be acquired % (0 seconds after, without a delay). Is that correct? % % Q2? - Can I find the slice acquisition time in the minc files? %_______________________________________________________________ numslices = 28; interslice = 0.092; % Descending order slicetimes = ((numslices - 1):-1:0) * interslice; % Takes care of the interleaved acquisition slicetimes_odd = slicetimes(1:numslices/2); slicetimes_even = slicetimes(numslices/2+1:numslices); slicetimes(1:2:numslices) = slicetimes_odd; slicetimes(2:2:numslices) = slicetimes_even; % events is a matrix of events whose rows are events % and columns are: % 1- events ids: an integer from 1 to N=number of events, to identify % the event type. % 2- event times: start of event, synchronized with frame and slice times. % 3- durations: (optional, default is 0) duration of the event. % 4- heights: (optional, default is 1) height of response for event. % % Here, events ids correspond to: % 1 <=> Word, high imageability % 2 <=> Word, low imageability % 3 <=> Non-Word % 4 <=> Baseline (strings of same letters in capital or small letters) % % The onset values and durations were extracted from the % stimuli presentation program. Here we use the ISI for the % durations and the target onset times for the event times. % Other choices are possible for the durations.... % events has 120 rows, since there are 120 stimuli in this run. events = [ 2 36.338 2.25 1 4 38.606 2.0 1 2 40.606 2.5 1 1 43.106 2.25 1 3 45.356 2.0 1 1 47.356 3.0 1 4 50.356 2.75 1 1 53.106 3.0 1 4 56.106 2.0 1 3 58.106 3.0 1 3 61.106 2.0 1 ... 1 324.606 3.0 1 4 327.606 2.75 1 1 330.356 2.0 1 2 332.356 2.5 1] %__________________________________________________________ % % Q? - When to include the baseline in the condition, % when not to? What is the rational behind that choice? % This has an impact on how we define the contrast matrix (see below) %___________________________________________________________ % Making the design matrices using fmridesign X_cache=fmridesign(frametimes,slicetimes,events); % Defining contrasts % A matrix whose rows are contrasts for the statistic images (for the % response variables) with row length equals to number of regressors % variables in X_cache, and columns are the contrasts. % % For example here (regardless of the correctness of the subject answer), % if were are interested in the regions of the brain activated when % high imageability words are presented, i.e. condition 1 minus % the baseline, we would define this contrast in the following manner: contrast = [ 1 0 0 -1] % contrast is a matrix with 4 columns (since there are 4 conditions, 4 regressors) % Frames to exclude from the analysis: % - First few frames of functional run (not steady-state image) % - other frames where there is motion % Here the study ask to remove the first 3 frames. exclude=[1 2 3]; %______________________________________________________________________ % % Q? - If we want to exclude frames during which the subject moved a lot % we need to find out first. xdisp with TIC function allows us to see a % movie of frames. How to interpret the plot produced by xdisp ? %______________________________________________________________________ % Logical matrix indicating output statistics by 1. Rows correspond % to rows of contrast, columns correspond to desired statistics. which_stats=[1 1 1 1 0 0 0 0 0]; input_file='ida-ab171292-sonata-21247-20040314-100032-4-mri_MC.mnc'; output_file_base=['ida-ab171292-sonata-21247-20040314-100032-4-mri_C1 '; 'ida-ab171292-sonata-21247-20040314-100032-4-mri_C2MC3'] % fwhm in mm of a 3D Gaussian smoothing kernel: fwhm_rho = 15; [df1 p]=fmrilm(input_file, output_file_base, X_cache, contrast, exclude, which_s tats); ----------------------------------------------- And I got the following error: ??? Index exceeds matrix dimensions. Error in ==> /usr/local/matlab61/toolbox/fmri/fmrilm.m On line 381 ==> X=[squeeze(X_cache.X(keep,:,1,slice)) Trend(:,:,slice)]; Error in ==> /data/scratch1/yves/batch_ana.m On line 249 ==> [df1 p]=fmrilm(input_file, output_file_base, X_cache, contrast, exclude, which_stats); __________________________________________ Many thanks Yves