help > Error at segmentation step
Showing 1-4 of 4 posts
Apr 19, 2017 10:04 PM | Tatyana Mukhina
Error at segmentation step
Hello everyone,
I'm getting an error at the segmentation (Setup, 2/7) step while makeing a group analysis. The program creates new .nii files in structure data and shows an error message that corresponding .img file doesn't exist.
I don't know how to fix this error.
ERROR DESCRIPTION:
Error using spm_vol>spm_vol_hdr (line 80)
File "E:\Group_5\Left\Data\Akhmedov\structure\c320140701_100711BRAINSTD23s003a1001.img" does not exist.
Error in spm_vol (line 61)
v = spm_vol_hdr(deblank(P(i,:)));
Error in conn_getinfo (line 18)
V=spm_vol(filename);
Error in conn_file (line 3)
[V,str,icon,filename]=conn_getinfo(filename);
Error in conn_process (line 238)
CONN_x.Setup.rois.files{nsub}{n1}{nses}=conn_file(ffile);
Error in conn_process (line 14)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 2977)
else conn_process('setup');
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.15.h
SPM12 + DEM FieldMap MEEGtools wfupickatlas
Matlab v.2015b
storage: 93.7Gb available
Thanks.
Best,
Tatyana
I'm getting an error at the segmentation (Setup, 2/7) step while makeing a group analysis. The program creates new .nii files in structure data and shows an error message that corresponding .img file doesn't exist.
I don't know how to fix this error.
ERROR DESCRIPTION:
Error using spm_vol>spm_vol_hdr (line 80)
File "E:\Group_5\Left\Data\Akhmedov\structure\c320140701_100711BRAINSTD23s003a1001.img" does not exist.
Error in spm_vol (line 61)
v = spm_vol_hdr(deblank(P(i,:)));
Error in conn_getinfo (line 18)
V=spm_vol(filename);
Error in conn_file (line 3)
[V,str,icon,filename]=conn_getinfo(filename);
Error in conn_process (line 238)
CONN_x.Setup.rois.files{nsub}{n1}{nses}=conn_file(ffile);
Error in conn_process (line 14)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 2977)
else conn_process('setup');
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.15.h
SPM12 + DEM FieldMap MEEGtools wfupickatlas
Matlab v.2015b
storage: 93.7Gb available
Thanks.
Best,
Tatyana
Apr 20, 2017 04:04 AM | Alfonso Nieto-Castanon - Boston University
RE: Error at segmentation step
Hi Tatyana,
Thanks for reporting this, that was a bug that we had not run into before. If you could please update to the latest release and install the attached patch (this patch is for 17c, simply copy this file to the conn distribution folder overwriting the file with the same name there) that should fix it. Let me know if you run into any issues.
Note: if you prefer to keep your current version (you are currently using a somewhat old CONN release, 15h) let me know and I will send you a specific patch for that version.
Best
Alfonso
Originally posted by Tatyana Mukhina:
Thanks for reporting this, that was a bug that we had not run into before. If you could please update to the latest release and install the attached patch (this patch is for 17c, simply copy this file to the conn distribution folder overwriting the file with the same name there) that should fix it. Let me know if you run into any issues.
Note: if you prefer to keep your current version (you are currently using a somewhat old CONN release, 15h) let me know and I will send you a specific patch for that version.
Best
Alfonso
Originally posted by Tatyana Mukhina:
Hello everyone,
I'm getting an error at the segmentation (Setup, 2/7) step while makeing a group analysis. The program creates new .nii files in structure data and shows an error message that corresponding .img file doesn't exist.
I don't know how to fix this error.
ERROR DESCRIPTION:
Error using spm_vol>spm_vol_hdr (line 80)
File "E:\Group_5\Left\Data\Akhmedov\structure\c320140701_100711BRAINSTD23s003a1001.img" does not exist.
Error in spm_vol (line 61)
v = spm_vol_hdr(deblank(P(i,:)));
Error in conn_getinfo (line 18)
V=spm_vol(filename);
Error in conn_file (line 3)
[V,str,icon,filename]=conn_getinfo(filename);
Error in conn_process (line 238)
CONN_x.Setup.rois.files{nsub}{n1}{nses}=conn_file(ffile);
Error in conn_process (line 14)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 2977)
else conn_process('setup');
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.15.h
SPM12 + DEM FieldMap MEEGtools wfupickatlas
Matlab v.2015b
storage: 93.7Gb available
Thanks.
Best,
Tatyana
I'm getting an error at the segmentation (Setup, 2/7) step while makeing a group analysis. The program creates new .nii files in structure data and shows an error message that corresponding .img file doesn't exist.
I don't know how to fix this error.
ERROR DESCRIPTION:
Error using spm_vol>spm_vol_hdr (line 80)
File "E:\Group_5\Left\Data\Akhmedov\structure\c320140701_100711BRAINSTD23s003a1001.img" does not exist.
Error in spm_vol (line 61)
v = spm_vol_hdr(deblank(P(i,:)));
Error in conn_getinfo (line 18)
V=spm_vol(filename);
Error in conn_file (line 3)
[V,str,icon,filename]=conn_getinfo(filename);
Error in conn_process (line 238)
CONN_x.Setup.rois.files{nsub}{n1}{nses}=conn_file(ffile);
Error in conn_process (line 14)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 2977)
else conn_process('setup');
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.15.h
SPM12 + DEM FieldMap MEEGtools wfupickatlas
Matlab v.2015b
storage: 93.7Gb available
Thanks.
Best,
Tatyana
Apr 28, 2017 08:04 AM | Tatyana Mukhina
RE: Error at segmentation step
Good morning, Alfonso.
I can't download Conn 17c now because the site is in read-only mode, so I can't test your patch. Anyway, I've been doing my analysis with version 15h, so I'd be very grateful if you provide a patch for this version.
Thank you.
Best,
Tatyana.
I can't download Conn 17c now because the site is in read-only mode, so I can't test your patch. Anyway, I've been doing my analysis with version 15h, so I'd be very grateful if you provide a patch for this version.
Thank you.
Best,
Tatyana.
May 3, 2017 09:05 PM | Tatyana Mukhina
RE: Error at segmentation step
Hello.
I tried to do analysis with patched conn 17c, but I got new error at Setup step.
Could you please fix it and provide a patch for version 15h as we're using this specific version in our organization. Thank you.
ERROR DESCRIPTION:
Undefined function or variable 'Nstep2'.
Error in conn_process (line 634)
if QASTEP2, CONN_x.Setup.l2covariates.values{nsub}{qa_icov}=Nstep2;
Error in conn_process (line 16)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 4119)
else conn_process('setup'); ispending=false;
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.17.c
SPM12 + DEM FieldMap MEEGtools wfupickatlas
Matlab v.2015b
storage: 129.8Gb available
spm installed in folder C:\Program Files\MATLAB\R2015b\toolbox\spm12
conn installed in folder C:\Program Files\MATLAB\R2015b\toolbox\conn
Best,
Tatyana
I tried to do analysis with patched conn 17c, but I got new error at Setup step.
Could you please fix it and provide a patch for version 15h as we're using this specific version in our organization. Thank you.
ERROR DESCRIPTION:
Undefined function or variable 'Nstep2'.
Error in conn_process (line 634)
if QASTEP2, CONN_x.Setup.l2covariates.values{nsub}{qa_icov}=Nstep2;
Error in conn_process (line 16)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 4119)
else conn_process('setup'); ispending=false;
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.17.c
SPM12 + DEM FieldMap MEEGtools wfupickatlas
Matlab v.2015b
storage: 129.8Gb available
spm installed in folder C:\Program Files\MATLAB\R2015b\toolbox\spm12
conn installed in folder C:\Program Files\MATLAB\R2015b\toolbox\conn
Best,
Tatyana