[MINC-users] MINC-users Digest, Vol 131, Issue 14
Soren Christensen
sorench at gmail.com
Wed Aug 17 14:09:28 EDT 2016
Thanks for posting. I had the same issue. Based on your mod it seems the
source fix is to change lines 55 ad 61
in minctools/conversion/CMakeLists.txt
and move ${ZNZ_LIBRARY} to the left of ${LIBMINC_LIBRARIES}. At leas that
seems to work for me.
Soren
On Thu, Jul 28, 2016 at 7:18 PM, Thomas Funck, Mr <
thomas.funck at mail.mcgill.ca> wrote:
> Compiling ZLIB before the rest didn't work, but I found a rather hacky
> workaround.
>
>
> In the following files the path to libz.a has to be moved to be behind the
> path to libznz.a.
>
>
> ./minctools/conversion/CMakeFiles/nii2mnc.dir/link.txt
> ./minctools/conversion/CMakeFiles/mnc2nii.dir/link.txt
>
> After that the compilation works.
>
> Thomas
>
>
> ________________________________
> From: minc-users-bounces at bic.mni.mcgill.ca <minc-users-bounces at bic.mni.
> mcgill.ca> on behalf of minc-users-request at bic.mni.mcgill.ca <
> minc-users-request at bic.mni.mcgill.ca>
> Sent: Wednesday, July 27, 2016 12:00:01 PM
> To: minc-users at bic.mni.mcgill.ca
> Subject: MINC-users Digest, Vol 131, Issue 14
>
> Send MINC-users mailing list submissions to
> minc-users at bic.mni.mcgill.ca
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> or, via email, send a message with subject or body 'help' to
> minc-users-request at bic.mni.mcgill.ca
>
> You can reach the person managing the list at
> minc-users-owner at bic.mni.mcgill.ca
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of MINC-users digest..."
>
>
> Today's Topics:
>
> 1. dcm2mnc error regarding PatientAge (Daniel Marchand)
> 2. Problem with ZLIB when compiling minc-toolkit-v2
> (Thomas Funck, Mr)
> 3. Re: Problem with ZLIB when compiling minc-toolkit-v2
> (vladimir.fonov at gmail.com)
> 4. Re: dcm2mnc error regarding PatientAge (Robert D. Vincent)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 26 Jul 2016 13:05:35 -0400
> From: Daniel Marchand <daniel at biospective.com>
> To: minc-users at bic.mni.mcgill.ca
> Subject: [MINC-users] dcm2mnc error regarding PatientAge
> Message-ID:
> <CALZEBsYNOnpxS-opkovO6mJFu1Xf-a1BeHjHNYbdPxNPLdz0Uw at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> I'm having trouble converting a dicom file including the line:
> (0010,1010) AS [0000] # 4, 1 PatientAge
>
> which throws the error:
> Age units (0000) unknown
>
> It seems that the cause of the error is
> inside of conversion/dcm2mnc/minc_file.c :
>
> if (strlen(general_info->patient.age) > 0) {
> string_t temp;
> int i;
> double age;
>
> strncpy(temp, general_info->patient.age, STRING_T_LEN - 1);
> while (temp[i] != 0 && !isdigit(temp[i]))
> i++;
> if (temp[i] == 0) {
> fprintf(stderr, "ERROR: Age was not numeric!!\n");
> exit(-1);
> }
> age = atof(&temp[i]);
> while (temp[i] != 0 && isdigit(temp[i]))
> i++;
> if (temp[i] == 'M') /* age is in months */
> age /= 12.0;
> else if (temp[i] == 'W') /* age is in weeks */
> age /= 52.0;
> else if (temp[i] == 'D') /* age is in days */
> age /= 365.0;
> else if (temp[i] != 'Y') { /* age is in years */
> fprintf(stderr, "ERROR: Age units (%s) unknown.\n", temp);
> exit(-1);
> }
> miattputdbl(mincid, varid, MIage, age);
>
> I would appear that perhaps a new option could be added where
> dcm2mnc doesn't crash if the age is written as [0000]?
>
> Best,
>
> Daniel
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 26 Jul 2016 18:36:14 +0000
> From: "Thomas Funck, Mr" <thomas.funck at mail.mcgill.ca>
> To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
> Subject: [MINC-users] Problem with ZLIB when compiling minc-toolkit-v2
> Message-ID:
> <BN3PR03MB1445BC1E1A497B51E9AB82E1A60E0 at BN3PR03MB1445.
> namprd03.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I'm trying to compile minc-toolkit-v2, but ran into the following problem.
> I'm trying to compile on Ubuntu 16.04.1 LTS and with USE_SYSTEM_ZLIB=OFF. I
> also tried minc-toolkit but ran into the same error.
>
> Thanks for any help,
>
> Thomas
>
> Scanning dependencies of target nii2mnc
> [ 23%] Building C object minctools/conversion/
> CMakeFiles/nii2mnc.dir/nifti1/nii2mnc.c.o
> [ 23%] Linking C executable nii2mnc
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzopen':
> znzlib.c:(.text+0x4a): undefined reference to `gzopen'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzdopen':
> znzlib.c:(.text+0x102): undefined reference to `gzdopen'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `Xznzclose':
> znzlib.c:(.text+0x166): undefined reference to `gzclose'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzread':
> znzlib.c:(.text+0x220): undefined reference to `gzread'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzwrite':
> znzlib.c:(.text+0x320): undefined reference to `gzwrite'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzseek':
> znzlib.c:(.text+0x3db): undefined reference to `gzseek'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzrewind':
> znzlib.c:(.text+0x447): undefined reference to `gzseek'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znztell':
> znzlib.c:(.text+0x4a3): undefined reference to `gztell'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzputs':
> znzlib.c:(.text+0x4f7): undefined reference to `gzputs'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzgets':
> znzlib.c:(.text+0x55b): undefined reference to `gzgets'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzflush':
> znzlib.c:(.text+0x5c5): undefined reference to `gzflush'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzeof':
> znzlib.c:(.text+0x623): undefined reference to `gzeof'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzputc':
> znzlib.c:(.text+0x677): undefined reference to `gzputc'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzgetc':
> znzlib.c:(.text+0x6f5): undefined reference to `gzgetc'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzprintf':
> znzlib.c:(.text+0x798): undefined reference to `gzprintf'
> collect2: error: ld returned 1 exit status
> minctools/conversion/CMakeFiles/nii2mnc.dir/build.make:105: recipe for
> target 'minctools/conversion/nii2mnc' failed
> make[2]: *** [minctools/conversion/nii2mnc] Error 1
> CMakeFiles/Makefile2:5017: recipe for target 'minctools/conversion/CMakeFiles/nii2mnc.dir/all'
> failed
> make[1]: *** [minctools/conversion/CMakeFiles/nii2mnc.dir/all] Error 2
> Makefile:160: recipe for target 'all' failed
> make: *** [all] Error 2
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 26 Jul 2016 14:43:17 -0400
> From: vladimir.fonov at gmail.com
> To: MINC list <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] Problem with ZLIB when compiling
> minc-toolkit-v2
> Message-ID: <64C52D64-4ED0-4241-A956-8952D5B37DF9 at gmail.com>
> Content-Type: text/plain; charset=utf-8
>
> Can you try running ?make ZLIB? first , and then ?make nii2mnc? ?
>
>
> > On Jul 26, 2016, at 14:36, Thomas Funck, Mr <thomas.funck at mail.mcgill.ca>
> wrote:
> >
> > Hi,
> >
> > I'm trying to compile minc-toolkit-v2, but ran into the following
> problem. I'm trying to compile on Ubuntu 16.04.1 LTS and with
> USE_SYSTEM_ZLIB=OFF. I also tried minc-toolkit but ran into the same error.
> >
> > Thanks for any help,
> >
> > Thomas
> >
> > Scanning dependencies of target nii2mnc
> > [ 23%] Building C object minctools/conversion/
> CMakeFiles/nii2mnc.dir/nifti1/nii2mnc.c.o
> > [ 23%] Linking C executable nii2mnc
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzopen':
> > znzlib.c:(.text+0x4a): undefined reference to `gzopen'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzdopen':
> > znzlib.c:(.text+0x102): undefined reference to `gzdopen'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `Xznzclose':
> > znzlib.c:(.text+0x166): undefined reference to `gzclose'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzread':
> > znzlib.c:(.text+0x220): undefined reference to `gzread'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzwrite':
> > znzlib.c:(.text+0x320): undefined reference to `gzwrite'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzseek':
> > znzlib.c:(.text+0x3db): undefined reference to `gzseek'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzrewind':
> > znzlib.c:(.text+0x447): undefined reference to `gzseek'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znztell':
> > znzlib.c:(.text+0x4a3): undefined reference to `gztell'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzputs':
> > znzlib.c:(.text+0x4f7): undefined reference to `gzputs'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzgets':
> > znzlib.c:(.text+0x55b): undefined reference to `gzgets'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzflush':
> > znzlib.c:(.text+0x5c5): undefined reference to `gzflush'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzeof':
> > znzlib.c:(.text+0x623): undefined reference to `gzeof'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzputc':
> > znzlib.c:(.text+0x677): undefined reference to `gzputc'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzgetc':
> > znzlib.c:(.text+0x6f5): undefined reference to `gzgetc'
> > ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function
> `znzprintf':
> > znzlib.c:(.text+0x798): undefined reference to `gzprintf'
> > collect2: error: ld returned 1 exit status
> > minctools/conversion/CMakeFiles/nii2mnc.dir/build.make:105: recipe for
> target 'minctools/conversion/nii2mnc' failed
> > make[2]: *** [minctools/conversion/nii2mnc] Error 1
> > CMakeFiles/Makefile2:5017: recipe for target 'minctools/conversion/CMakeFiles/nii2mnc.dir/all'
> failed
> > make[1]: *** [minctools/conversion/CMakeFiles/nii2mnc.dir/all] Error 2
> > Makefile:160: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> Best regards, Vladimir S. FONOV ~ v.s.fonov <at> ilmarin.info
>
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 26 Jul 2016 23:36:34 -0400
> From: "Robert D. Vincent" <robert.d.vincent at mcgill.ca>
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] dcm2mnc error regarding PatientAge
> Message-ID:
> <CAAd5DeQz2bmP8UkREuQeOA3WJDxoyLnhcW59JiycLpoV-YFNSw at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> I'll relax the test and make it a warning. But the AS VR does not permit a
> field value of 0000.
>
> -bert
>
> On Tue, Jul 26, 2016 at 1:05 PM, Daniel Marchand <daniel at biospective.com>
> wrote:
>
> > Hi,
> >
> > I'm having trouble converting a dicom file including the line:
> > (0010,1010) AS [0000] # 4, 1
> PatientAge
> >
> > which throws the error:
> > Age units (0000) unknown
> >
> > It seems that the cause of the error is
> > inside of conversion/dcm2mnc/minc_file.c :
> >
> > if (strlen(general_info->patient.age) > 0) {
> > string_t temp;
> > int i;
> > double age;
> >
> > strncpy(temp, general_info->patient.age, STRING_T_LEN - 1);
> > while (temp[i] != 0 && !isdigit(temp[i]))
> > i++;
> > if (temp[i] == 0) {
> > fprintf(stderr, "ERROR: Age was not numeric!!\n");
> > exit(-1);
> > }
> > age = atof(&temp[i]);
> > while (temp[i] != 0 && isdigit(temp[i]))
> > i++;
> > if (temp[i] == 'M') /* age is in months */
> > age /= 12.0;
> > else if (temp[i] == 'W') /* age is in weeks */
> > age /= 52.0;
> > else if (temp[i] == 'D') /* age is in days */
> > age /= 365.0;
> > else if (temp[i] != 'Y') { /* age is in years */
> > fprintf(stderr, "ERROR: Age units (%s) unknown.\n", temp);
> > exit(-1);
> > }
> > miattputdbl(mincid, varid, MIage, age);
> >
> > I would appear that perhaps a new option could be added where
> > dcm2mnc doesn't crash if the age is written as [0000]?
> >
> > Best,
> >
> > Daniel
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> ------------------------------
>
> _______________________________________________
> MINC-users mailing list
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
> End of MINC-users Digest, Vol 131, Issue 14
> *******************************************
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
More information about the MINC-users
mailing list