Dear all,
I've come across a similar problem to the one described before in qdec, but cannot find a solution for it,
I've previously visualised my data using qdec, but when I tried to run it again I get the following error. I've checked to make sure my subject is named correctly and I am in the correct subject directory. Any help will be great appreciated,
gdfReadHeader: reading /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde c.fsgd ERROR: gdfRead: /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde c.fsgd is not formatted properly. The first string is 'q&@', should be 'GroupDescriptorFile' Error in Analyze: command failed: mri_glmfit --y /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/y.m gh --fsgd /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde c.fsgd --glmdir /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled --surf fsaverage lh --C /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con trasts/Avg-Intercept.mat --C /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con trasts/Avg-thickness-dig_back-Cor.mat --C /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con trasts/Avg-thickness-educ-Cor.mat
Thanks,
Prapti
----------
Message: 7 Date: Mon, 08 Dec 2008 11:43:28 -0500 From: Nick Schmansky nicks@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec message To: juliaaltenburg@yahoo.de Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Message-ID: 1228754609.6864.17.camel@minerva.nmr.mgh.harvard.edu Content-Type: text/plain
Julia,
Does it give any further details in the error message? It would be in the terminal output (the popup box would not have the full message). Do all of those files in the command line exist and are readable?
You can also try copy-and-pasting that command directly to the terminal (outside of qdec) to see what error message it displays.
Nick
On Mon, 2008-12-08 at 10:57 +0000, Julia Altenburg wrote:
Hey all,
I'm getting the following message while using qdec
Error in Analyze: command failed: mri_glmfit --y
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/y.mgh --fsgd /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/qdec. fsgd dods --glmdir /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled --surf fsaverage lh --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Avg-Intercept-thickness.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Avg-thickness-alter-Cor.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Diff-BPD-KG-Intercept-thickness.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Diff-BPD-KG-Cor-thickness-alter.mat
I've a qdec.table and a fsgd.file included in my subject folder. Do I have to type a command to get the fsgd. file connected? I'm not really sure what causes the error. While using an older
freesurfer version on a different mac this (but some other) error doesn't show up.
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.1.0
Kernel info: Darwin 8.11.1 i386
Thank you in advance Cheers Julia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 8 Date: Mon, 08 Dec 2008 12:51:32 -0500 From: Doug Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Statistic analysing for a mask To: Alexandru Hanganu hanganu.alexandru@yahoo.de Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Message-ID: 493D5EA4.5050905@nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd lines.
doug
Alexandru Hanganu wrote:
Dear Freesurfer users,
We have an MNI mask and we want to apply this mask on a group of subjects for small volume correction. so we did the following steps:
- cd $SUBJECTS_DIR/fsaverage/surf
fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat
- cd $SUBJECTS_DIR/fsaverage/surf
mri_vol2surf --mov /path/to/ROI5.nii --reg TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fsaverage.ROI5.mgh
- cd $SUBJECTS_DIR/subjid/surf
mri_surf2surf --s subjid --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh . . . Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 147410, nTrgMulti = 16432, MnTrgMultiHits = 2.25237 nSrc121 = 86069, nSrcLost = 0, nSrcMulti = 42416, MnSrcMultiHits =
2.31875 Saving target data
- Next step was just for verifying, but we received an error (maybe
it's not so important): cd $SUBJECTS_DIR/subjid/surf mri_segstats --seg $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh --in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt
Loading /usr/local/freesurfer/subjects/fsaverage/surf/lh.fsaverage.ROI5.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg
We want to determine the statistics only for this mask for the whole group of subjects (qdec, or mri_glmfit). If the mapping of our subjects thickness data was good, what should we
do next in order to achieve our goal ?
Thank you.
Best regards, Dr. Alexandru Hanganu ___________________________________ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.
-
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Prapti,
Try deleting the directory 'qdec/Untitled' and run it again. Prior to v4.2.0, qdec did not delete that directory, which is the default working directory, so its possible some incompatible files from a prior run were lingering.
Nick
On Thu, 2009-03-05 at 09:42 +1100, Prapti Gautam wrote:
Dear all,
I've come across a similar problem to the one described before in qdec, but cannot find a solution for it,
I've previously visualised my data using qdec, but when I tried to run it again I get the following error. I've checked to make sure my subject is named correctly and I am in the correct subject directory. Any help will be great appreciated,
gdfReadHeader: reading /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde c.fsgd ERROR: gdfRead: /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde c.fsgd is not formatted properly. The first string is 'q&@', should be 'GroupDescriptorFile' Error in Analyze: command failed: mri_glmfit --y /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/y.m gh --fsgd /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde c.fsgd --glmdir /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled --surf fsaverage lh --C /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con trasts/Avg-Intercept.mat --C /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con trasts/Avg-thickness-dig_back-Cor.mat --C /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con trasts/Avg-thickness-educ-Cor.mat
Thanks,
Prapti
Message: 7 Date: Mon, 08 Dec 2008 11:43:28 -0500 From: Nick Schmansky nicks@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec message To: juliaaltenburg@yahoo.de Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Message-ID: 1228754609.6864.17.camel@minerva.nmr.mgh.harvard.edu Content-Type: text/plain
Julia,
Does it give any further details in the error message? It would be in the terminal output (the popup box would not have the full message). Do all of those files in the command line exist and are readable?
You can also try copy-and-pasting that command directly to the terminal (outside of qdec) to see what error message it displays.
Nick
On Mon, 2008-12-08 at 10:57 +0000, Julia Altenburg wrote:
Hey all,
I'm getting the following message while using qdec
Error in Analyze: command failed: mri_glmfit --y
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/y.mgh --fsgd /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/qdec. fsgd dods --glmdir /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled --surf fsaverage lh --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Avg-Intercept-thickness.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Avg-thickness-alter-Cor.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Diff-BPD-KG-Intercept-thickness.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Diff-BPD-KG-Cor-thickness-alter.mat
I've a qdec.table and a fsgd.file included in my subject folder. Do I have to type a command to get the fsgd. file connected? I'm not really sure what causes the error. While using an older
freesurfer version on a different mac this (but some other) error doesn't show up.
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.1.0
Kernel info: Darwin 8.11.1 i386
Thank you in advance Cheers Julia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Message: 8 Date: Mon, 08 Dec 2008 12:51:32 -0500 From: Doug Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Statistic analysing for a mask To: Alexandru Hanganu hanganu.alexandru@yahoo.de Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Message-ID: 493D5EA4.5050905@nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd lines.
doug
Alexandru Hanganu wrote:
Dear Freesurfer users,
We have an MNI mask and we want to apply this mask on a group of subjects for small volume correction. so we did the following steps:
- cd $SUBJECTS_DIR/fsaverage/surf
fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat
- cd $SUBJECTS_DIR/fsaverage/surf
mri_vol2surf --mov /path/to/ROI5.nii --reg TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fsaverage.ROI5.mgh
- cd $SUBJECTS_DIR/subjid/surf
mri_surf2surf --s subjid --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh . . . Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 147410, nTrgMulti = 16432, MnTrgMultiHits = 2.25237 nSrc121 = 86069, nSrcLost = 0, nSrcMulti = 42416, MnSrcMultiHits =
2.31875 Saving target data
- Next step was just for verifying, but we received an error (maybe
it's not so important): cd $SUBJECTS_DIR/subjid/surf mri_segstats --seg $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh --in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt
Loading /usr/local/freesurfer/subjects/fsaverage/surf/lh.fsaverage.ROI5.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg
We want to determine the statistics only for this mask for the whole group of subjects (qdec, or mri_glmfit). If the mapping of our subjects thickness data was good, what should we
do next in order to achieve our goal ?
Thank you.
Best regards, Dr. Alexandru Hanganu ___________________________________ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Deleting 'qdec/Untitled' worked! Thanks,
Prapti
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thursday, 5 March 2009 11:10 AM To: Prapti Gautam Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] qdec error in analyze
Prapti,
Try deleting the directory 'qdec/Untitled' and run it again. Prior to v4.2.0, qdec did not delete that directory, which is the default working directory, so its possible some incompatible files from a prior run were lingering.
Nick
On Thu, 2009-03-05 at 09:42 +1100, Prapti Gautam wrote:
Dear all,
I've come across a similar problem to the one described before in
qdec,
but cannot find a solution for it,
I've previously visualised my data using qdec, but when I tried to run it again I get the following error. I've checked to make sure my
subject
is named correctly and I am in the correct subject directory. Any help will be great appreciated,
gdfReadHeader: reading
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
c.fsgd ERROR: gdfRead:
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
c.fsgd is not formatted properly. The first string is 'q&@', should be 'GroupDescriptorFile' Error in Analyze: command failed: mri_glmfit --y
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/y.m
gh --fsgd
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
c.fsgd --glmdir /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled --surf fsaverage lh --C
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
trasts/Avg-Intercept.mat --C
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
trasts/Avg-thickness-dig_back-Cor.mat --C
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
trasts/Avg-thickness-educ-Cor.mat
Thanks,
Prapti
Message: 7 Date: Mon, 08 Dec 2008 11:43:28 -0500 From: Nick Schmansky nicks@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec message To: juliaaltenburg@yahoo.de Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Message-ID: 1228754609.6864.17.camel@minerva.nmr.mgh.harvard.edu Content-Type: text/plain
Julia,
Does it give any further details in the error message? It would be in the terminal output (the popup box would not have the full message).
Do
all of those files in the command line exist and are readable?
You can also try copy-and-pasting that command directly to the
terminal
(outside of qdec) to see what error message it displays.
Nick
On Mon, 2008-12-08 at 10:57 +0000, Julia Altenburg wrote:
Hey all,
I'm getting the following message while using qdec
Error in Analyze: command failed: mri_glmfit --y
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/y.mgh
--fsgd
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/qdec.
fsgd dods --glmdir /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled --surf fsaverage lh --C
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
asts/lh-Avg-Intercept-thickness.mat --C
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
asts/lh-Avg-thickness-alter-Cor.mat --C
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
asts/lh-Diff-BPD-KG-Intercept-thickness.mat --C
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
asts/lh-Diff-BPD-KG-Cor-thickness-alter.mat
I've a qdec.table and a fsgd.file included in my subject folder. Do I have to type a command to get the fsgd. file connected? I'm not really sure what causes the error. While using an older
freesurfer version on a different mac this (but some other) error doesn't show up.
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.1.0
Kernel info: Darwin 8.11.1 i386
Thank you in advance Cheers Julia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Message: 8 Date: Mon, 08 Dec 2008 12:51:32 -0500 From: Doug Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Statistic analysing for a mask To: Alexandru Hanganu hanganu.alexandru@yahoo.de Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Message-ID: 493D5EA4.5050905@nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd
lines.
doug
Alexandru Hanganu wrote:
Dear Freesurfer users,
We have an MNI mask and we want to apply this mask on a group of subjects for small volume correction. so we did the following steps:
- cd $SUBJECTS_DIR/fsaverage/surf
fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat
- cd $SUBJECTS_DIR/fsaverage/surf
mri_vol2surf --mov /path/to/ROI5.nii --reg TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest
--hemi lh --out lh.fsaverage.ROI5.mgh
- cd $SUBJECTS_DIR/subjid/surf
mri_surf2surf --s subjid --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh . . . Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 147410, nTrgMulti = 16432, MnTrgMultiHits = 2.25237 nSrc121 = 86069, nSrcLost = 0, nSrcMulti = 42416, MnSrcMultiHits
=
2.31875 Saving target data
- Next step was just for verifying, but we received an error (maybe
it's not so important): cd $SUBJECTS_DIR/subjid/surf mri_segstats --seg
$SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh
--in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt
Loading /usr/local/freesurfer/subjects/fsaverage/surf/lh.fsaverage.ROI5.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg
We want to determine the statistics only for this mask for the whole
group of subjects (qdec, or mri_glmfit). If the mapping of our subjects thickness data was good, what should
we
do next in order to achieve our goal ?
Thank you.
Best regards, Dr. Alexandru Hanganu ___________________________________ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Good. I forgot to mention, the 'Design Name' entry box on the Design tab is intended for keep track of a particular analysis. For instance lets say your looking at thickness on the left hemi where you have selected diagnosis and age as factors. You might want to name the Design 'diagnosis_age_thickness_lh'. It will put the results in the $SUBJECTS_DIR/qdec/diagnosis_age_thickness_lh dir, which is handy as a way to save the results.
Nick
On Thu, 2009-03-05 at 11:30 +1100, Prapti Gautam wrote:
Deleting 'qdec/Untitled' worked! Thanks,
Prapti
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thursday, 5 March 2009 11:10 AM To: Prapti Gautam Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] qdec error in analyze
Prapti,
Try deleting the directory 'qdec/Untitled' and run it again. Prior to v4.2.0, qdec did not delete that directory, which is the default working directory, so its possible some incompatible files from a prior run were lingering.
Nick
On Thu, 2009-03-05 at 09:42 +1100, Prapti Gautam wrote:
Dear all,
I've come across a similar problem to the one described before in
qdec,
but cannot find a solution for it,
I've previously visualised my data using qdec, but when I tried to run it again I get the following error. I've checked to make sure my
subject
is named correctly and I am in the correct subject directory. Any help will be great appreciated,
gdfReadHeader: reading
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
c.fsgd ERROR: gdfRead:
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
c.fsgd is not formatted properly. The first string is 'q&@', should be 'GroupDescriptorFile' Error in Analyze: command failed: mri_glmfit --y
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/y.m
gh --fsgd
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
c.fsgd --glmdir /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled --surf fsaverage lh --C
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
trasts/Avg-Intercept.mat --C
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
trasts/Avg-thickness-dig_back-Cor.mat --C
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
trasts/Avg-thickness-educ-Cor.mat
Thanks,
Prapti
Message: 7 Date: Mon, 08 Dec 2008 11:43:28 -0500 From: Nick Schmansky nicks@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec message To: juliaaltenburg@yahoo.de Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Message-ID: 1228754609.6864.17.camel@minerva.nmr.mgh.harvard.edu Content-Type: text/plain
Julia,
Does it give any further details in the error message? It would be in the terminal output (the popup box would not have the full message).
Do
all of those files in the command line exist and are readable?
You can also try copy-and-pasting that command directly to the
terminal
(outside of qdec) to see what error message it displays.
Nick
On Mon, 2008-12-08 at 10:57 +0000, Julia Altenburg wrote:
Hey all,
I'm getting the following message while using qdec
Error in Analyze: command failed: mri_glmfit --y
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/y.mgh
--fsgd
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/qdec.
fsgd dods --glmdir /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled --surf fsaverage lh --C
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
asts/lh-Avg-Intercept-thickness.mat --C
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
asts/lh-Avg-thickness-alter-Cor.mat --C
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
asts/lh-Diff-BPD-KG-Intercept-thickness.mat --C
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
asts/lh-Diff-BPD-KG-Cor-thickness-alter.mat
I've a qdec.table and a fsgd.file included in my subject folder. Do I have to type a command to get the fsgd. file connected? I'm not really sure what causes the error. While using an older
freesurfer version on a different mac this (but some other) error doesn't show up.
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.1.0
Kernel info: Darwin 8.11.1 i386
Thank you in advance Cheers Julia
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Message: 8 Date: Mon, 08 Dec 2008 12:51:32 -0500 From: Doug Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Statistic analysing for a mask To: Alexandru Hanganu hanganu.alexandru@yahoo.de Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Message-ID: 493D5EA4.5050905@nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd
lines.
doug
Alexandru Hanganu wrote:
Dear Freesurfer users,
We have an MNI mask and we want to apply this mask on a group of subjects for small volume correction. so we did the following steps:
- cd $SUBJECTS_DIR/fsaverage/surf
fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat
- cd $SUBJECTS_DIR/fsaverage/surf
mri_vol2surf --mov /path/to/ROI5.nii --reg TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest
--hemi lh --out lh.fsaverage.ROI5.mgh
- cd $SUBJECTS_DIR/subjid/surf
mri_surf2surf --s subjid --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh . . . Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 147410, nTrgMulti = 16432, MnTrgMultiHits = 2.25237 nSrc121 = 86069, nSrcLost = 0, nSrcMulti = 42416, MnSrcMultiHits
=
2.31875 Saving target data
- Next step was just for verifying, but we received an error (maybe
it's not so important): cd $SUBJECTS_DIR/subjid/surf mri_segstats --seg
$SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh
--in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt
Loading /usr/local/freesurfer/subjects/fsaverage/surf/lh.fsaverage.ROI5.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg
We want to determine the statistics only for this mask for the whole
group of subjects (qdec, or mri_glmfit). If the mapping of our subjects thickness data was good, what should
we
do next in order to achieve our goal ?
Thank you.
Best regards, Dr. Alexandru Hanganu ___________________________________ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.
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-
Nick Schmansky -
Prapti Gautam