Dear Freesurfers,
So I have followed all the instructions given on your website in order to use qdec. When i analyse the images only using a file group.levels that defines the two groups I'm comparing the analysis runs fine and gives me results, but when I add gender, for instance, as a discrete factor, it loads the data successfully but when I click analyse it shows the following error:
Error in Analyze: Couldn't open file /tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/lh.thickness.fwhm10.fsaverage.mgh
Please guide me as to what is going wrong and what I can do to fix it. I would appreciate a quick response as my thesis submission is due in two weeks and I cannot proceed until this problem is sorted.
Thanks and regards, Saloni
Hi Saloni
Does that directory exist? What is your SUBJECTS_DIR set to? And have you run recon-all -qcache on all your subjects?
cheers Bruce On Mon, 26 May 2014, Saloni Sharma wrote:
Dear Freesurfers,
So I have followed all the instructions given on your website in order to use qdec. When i analyse the images only using a file group.levels that defines the two groups I'm comparing the analysis runs fine and gives me results, but when I add gender, for instance, as a discrete factor, it loads the data successfully but when I click analyse it shows the following error:
Error in Analyze: Couldn't open file/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/lh.t hickness.fwhm10.fsaverage.mgh
Please guide me as to what is going wrong and what I can do to fix it. I would appreciate a quick response as my thesis submission is due in two weeks and I cannot proceed until this problem is sorted.
Thanks and regards, Saloni
Hey Bruce,
Yes, that directory exists, as I said if I only choose groups(high stress and low stress) as the discrete variables its runs fine and analyses, it only shows the error if I add more factors (like gender) into the software.
My subjects directory is set to export SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/
and yes I have run recon-all-qcache on all my subjects.
Saloni
On 26 May 2014 16:58, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Saloni
Does that directory exist? What is your SUBJECTS_DIR set to? And have you run recon-all -qcache on all your subjects?
cheers Bruce On Mon, 26 May 2014, Saloni Sharma wrote:
Dear Freesurfers,
So I have followed all the instructions given on your website in order to use qdec. When i analyse the images only using a file group.levels that defines the two groups I'm comparing the analysis runs fine and gives me results, but when I add gender, for instance, as a discrete factor, it
loads
the data successfully but when I click analyse it shows the following
error:
Error in Analyze: Couldn't open
file/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/lh.t
hickness.fwhm10.fsaverage.mgh
Please guide me as to what is going wrong and what I can do to fix it. I would appreciate a quick response as my thesis submission is due in two weeks and I cannot proceed until this problem is sorted.
Thanks and regards, Saloni
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
so if you click "analyze" without gender it works fine? Sorry, I missed that. I think you'll need to wait for Doug or Nick to reply, but you might send your qdec file and the group.levels files
sorry Bruce
On Mon, 26 May 2014, Saloni Sharma wrote:
Hey Bruce,
Yes, that directory exists, as I said if I only choose groups(high stress and low stress) as the discrete variables its runs fine and analyses, it only shows the error if I add more factors (like gender) into the software.
My subjects directory is set to export SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/
and yes I have run recon-all-qcache on all my subjects.
Saloni
On 26 May 2014 16:58, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Saloni
Does that directory exist? What is your SUBJECTS_DIR set to? And have you run recon-all -qcache on all your subjects? cheers Bruce On Mon, 26 May 2014, Saloni Sharma wrote: > Dear Freesurfers, > > So I have followed all the instructions given on your website in order to > use qdec. When i analyse the images only using a file group.levels that > defines the two groups I'm comparing the analysis runs fine and gives me > results, but when I add gender, for instance, as a discrete factor, it loads > the data successfully but when I click analyse it shows the following error: > > Error in Analyze: Couldn't openfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/ lh.t > hickness.fwhm10.fsaverage.mgh > > Please guide me as to what is going wrong and what I can do to fix it. I > would appreciate a quick response as my thesis submission is due in two > weeks and I cannot proceed until this problem is sorted. > > Thanks and regards, > Saloni > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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yes exactly, if I click analyze without the gender it works fine. No thats okay, what do you need from me again?
On 26 May 2014 17:11, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
so if you click "analyze" without gender it works fine? Sorry, I missed that. I think you'll need to wait for Doug or Nick to reply, but you might send your qdec file and the group.levels files
sorry Bruce
On Mon, 26 May 2014, Saloni Sharma wrote:
Hey Bruce,
Yes, that directory exists, as I said if I only choose groups(high stress and low stress) as the discrete variables its runs fine and analyses, it only shows the error if I add more factors (like gender) into the
software.
My subjects directory is set to export SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/
and yes I have run recon-all-qcache on all my subjects.
Saloni
On 26 May 2014 16:58, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Saloni
Does that directory exist? What is your SUBJECTS_DIR set to? And have you run recon-all -qcache on all your subjects? cheers Bruce On Mon, 26 May 2014, Saloni Sharma wrote: > Dear Freesurfers, > > So I have followed all the instructions given on your website in order to > use qdec. When i analyse the images only using a file group.levels that > defines the two groups I'm comparing the analysis runs fine and gives me > results, but when I add gender, for instance, as a discrete factor, it loads > the data successfully but when I click analyse it shows the following error: > > Error in Analyze: Couldn'topenfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/
lh.t > hickness.fwhm10.fsaverage.mgh > > Please guide me as to what is going wrong and what I can do to fix it. I > would appreciate a quick response as my thesis submission is due in two > weeks and I cannot proceed until this problem is sorted. > > Thanks and regards, > Saloni > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I am attaching a screen shot of the error, if it helps!
On 26 May 2014 17:14, Saloni Sharma sharmasa@tcd.ie wrote:
yes exactly, if I click analyze without the gender it works fine. No thats okay, what do you need from me again?
On 26 May 2014 17:11, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
so if you click "analyze" without gender it works fine? Sorry, I missed that. I think you'll need to wait for Doug or Nick to reply, but you might send your qdec file and the group.levels files
sorry Bruce
On Mon, 26 May 2014, Saloni Sharma wrote:
Hey Bruce,
Yes, that directory exists, as I said if I only choose groups(high
stress
and low stress) as the discrete variables its runs fine and analyses, it only shows the error if I add more factors (like gender) into the
software.
My subjects directory is set to export
SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/
and yes I have run recon-all-qcache on all my subjects.
Saloni
On 26 May 2014 16:58, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Saloni
Does that directory exist? What is your SUBJECTS_DIR set to? And have you run recon-all -qcache on all your subjects? cheers Bruce On Mon, 26 May 2014, Saloni Sharma wrote: > Dear Freesurfers, > > So I have followed all the instructions given on your website in order to > use qdec. When i analyse the images only using a file group.levels that > defines the two groups I'm comparing the analysis runs fine and gives me > results, but when I add gender, for instance, as a discrete factor, it loads > the data successfully but when I click analyse it shows the following error: > > Error in Analyze: Couldn'topenfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/
lh.t > hickness.fwhm10.fsaverage.mgh > > Please guide me as to what is going wrong and what I can do to fix it. I > would appreciate a quick response as my thesis submission is due in two > weeks and I cannot proceed until this problem is sorted. > > Thanks and regards, > Saloni > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Does it print out anything else? An alternative is to use the command line stream (create your own fsgd file, run mris_preproc, smooth, mri_glmfit, mri_glmfit-sim) doug
On 05/27/2014 06:38 AM, Saloni Sharma wrote:
I am attaching a screen shot of the error, if it helps!
On 26 May 2014 17:14, Saloni Sharma <sharmasa@tcd.ie mailto:sharmasa@tcd.ie> wrote:
yes exactly, if I click analyze without the gender it works fine. No thats okay, what do you need from me again? On 26 May 2014 17:11, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: so if you click "analyze" without gender it works fine? Sorry, I missed that. I think you'll need to wait for Doug or Nick to reply, but you might send your qdec file and the group.levels files sorry Bruce On Mon, 26 May 2014, Saloni Sharma wrote: > Hey Bruce, > > Yes, that directory exists, as I said if I only choose groups(high stress > and low stress) as the discrete variables its runs fine and analyses, it > only shows the error if I add more factors (like gender) into the software. > > My subjects directory is set to > export SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/ > > and yes I have run recon-all-qcache on all my subjects. > > Saloni > > > On 26 May 2014 16:58, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > Hi Saloni > > Does that directory exist? What is your SUBJECTS_DIR set to? And > have you > run recon-all -qcache on all your subjects? > > cheers > Bruce > On Mon, 26 May 2014, Saloni Sharma wrote: > > > Dear Freesurfers, > > > > So I have followed all the instructions given on your website > in order to > > use qdec. When i analyse the images only using a file > group.levels that > > defines the two groups I'm comparing the analysis runs fine > and gives me > > results, but when I add gender, for instance, as a discrete > factor, it loads > > the data successfully but when I click analyse it shows the > following error: > > > > Error in Analyze: Couldn't openfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/ > lh.t > > hickness.fwhm10.fsaverage.mgh > > > > Please guide me as to what is going wrong and what I can do to > fix it. I > > would appreciate a quick response as my thesis submission is > due in two > > weeks and I cannot proceed until this problem is sorted. > > > > Thanks and regards, > > Saloni > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It prints out fine and gives results if I only use it to analyse two groups(differentiated on stress levels) but if I add gender as a discrete variable or even as a continuous one along with the groups it shows this error.
Sent from my iPhone
On 27 May 2014, at 23:40, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Does it print out anything else? An alternative is to use the command line stream (create your own fsgd file, run mris_preproc, smooth, mri_glmfit, mri_glmfit-sim) doug
On 05/27/2014 06:38 AM, Saloni Sharma wrote: I am attaching a screen shot of the error, if it helps!
On 26 May 2014 17:14, Saloni Sharma <sharmasa@tcd.ie mailto:sharmasa@tcd.ie> wrote:
yes exactly, if I click analyze without the gender it works fine. No thats okay, what do you need from me again?
On 26 May 2014 17:11, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
so if you click "analyze" without gender it works fine? Sorry, I missed that. I think you'll need to wait for Doug or Nick to reply, but you might send your qdec file and the group.levels files sorry BruceOn Mon, 26 May 2014, Saloni Sharma wrote:Hey Bruce,
Yes, that directory exists, as I said if I only choose
groups(high stressand low stress) as the discrete variables its runs fine and
analyses, itonly shows the error if I add more factors (like gender)
into the software.My subjects directory is set to export
SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/and yes I have run recon-all-qcache on all my subjects.
Saloni
On 26 May 2014 16:58, Bruce Fischl
<fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:Hi Saloni Does that directory exist? What is your SUBJECTS_DIRset to? Andhave you run recon-all -qcache on all your subjects? cheers BruceOn Mon, 26 May 2014, Saloni Sharma wrote:Dear Freesurfers,
So I have followed all the instructions given on
your websitein order touse qdec. When i analyse the images only using a file
group.levels thatdefines the two groups I'm comparing the analysis
runs fineand gives meresults, but when I add gender, for instance, as a
discretefactor, it loadsthe data successfully but when I click analyse it
shows thefollowing error:Error in Analyze: Couldn't
openfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/lh.thickness.fwhm10.fsaverage.mgh
Please guide me as to what is going wrong and what I
can do tofix it. Iwould appreciate a quick response as my thesis
submission isdue in twoweeks and I cannot proceed until this problem is sorted.
Thanks and regards, Saloni
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the
person to whomit is addressed. If you believe this e-mail was sent to you in
error and thee-mail contains patient information, please contact the Partners
ComplianceHelpLine at http://www.partners.org/complianceline . If the e-mail was
sent to youin error but does not contain patient information, please contact the
senderand properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Saloni,
are you certain that you ran recon-qcache on subject 000054987500? the error message says that the file lh.thickness.fwhm10.fsaverage.mgh is missing, and this file is created by -qcache. i'd suggest running:
recon-all -s 000054987500 -qcache
then confirm that this file exists.
Nick
On Wed, 2014-05-28 at 01:21 +0100, Saloni wrote:
It prints out fine and gives results if I only use it to analyse two groups(differentiated on stress levels) but if I add gender as a discrete variable or even as a continuous one along with the groups it shows this error.
Sent from my iPhone
On 27 May 2014, at 23:40, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Does it print out anything else? An alternative is to use the command line stream (create your own fsgd file, run mris_preproc, smooth, mri_glmfit, mri_glmfit-sim) doug
On 05/27/2014 06:38 AM, Saloni Sharma wrote: I am attaching a screen shot of the error, if it helps!
On 26 May 2014 17:14, Saloni Sharma <sharmasa@tcd.ie mailto:sharmasa@tcd.ie> wrote:
yes exactly, if I click analyze without the gender it works fine. No thats okay, what do you need from me again?
On 26 May 2014 17:11, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
so if you click "analyze" without gender it works fine? Sorry, I missed that. I think you'll need to wait for Doug or Nick to reply, but you might send your qdec file and the group.levels files sorry BruceOn Mon, 26 May 2014, Saloni Sharma wrote:Hey Bruce,
Yes, that directory exists, as I said if I only choose
groups(high stressand low stress) as the discrete variables its runs fine and
analyses, itonly shows the error if I add more factors (like gender)
into the software.My subjects directory is set to export
SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/and yes I have run recon-all-qcache on all my subjects.
Saloni
On 26 May 2014 16:58, Bruce Fischl
<fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:Hi Saloni Does that directory exist? What is your SUBJECTS_DIRset to? Andhave you run recon-all -qcache on all your subjects? cheers BruceOn Mon, 26 May 2014, Saloni Sharma wrote:Dear Freesurfers,
So I have followed all the instructions given on
your websitein order touse qdec. When i analyse the images only using a file
group.levels thatdefines the two groups I'm comparing the analysis
runs fineand gives meresults, but when I add gender, for instance, as a
discretefactor, it loadsthe data successfully but when I click analyse it
shows thefollowing error:Error in Analyze: Couldn't
openfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/lh.thickness.fwhm10.fsaverage.mgh
Please guide me as to what is going wrong and what I
can do tofix it. Iwould appreciate a quick response as my thesis
submission isdue in twoweeks and I cannot proceed until this problem is sorted.
Thanks and regards, Saloni
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the
person to whomit is addressed. If you believe this e-mail was sent to you in
error and thee-mail contains patient information, please contact the Partners
ComplianceHelpLine at http://www.partners.org/complianceline . If the e-mail was
sent to youin error but does not contain patient information, please contact the
senderand properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Nick,
I am certain of it because the analysis runs fine when I analyze it with just a discrete variable group.levels...the moment I add factor.levels as another variable along with groups it gives me the error. And if I remove this particular subject from the data table(this subject is the first on the data list) and try running it again it shows the same error for the next subject on the list.
I am attaching a screen shot of the said file existing as well.
However, I am also running the command you gave again as we speak, just to see if it works.
On 28 May 2014 20:48, Nick Schmansky, MGH nicks@nmr.mgh.harvard.edu wrote:
Saloni,
are you certain that you ran recon-qcache on subject 000054987500? the error message says that the file lh.thickness.fwhm10.fsaverage.mgh is missing, and this file is created by -qcache. i'd suggest running:
recon-all -s 000054987500 -qcache
then confirm that this file exists.
Nick
On Wed, 2014-05-28 at 01:21 +0100, Saloni wrote:
It prints out fine and gives results if I only use it to analyse two
groups(differentiated on stress levels) but if I add gender as a discrete variable or even as a continuous one along with the groups it shows this error.
Sent from my iPhone
On 27 May 2014, at 23:40, Douglas N Greve greve@nmr.mgh.harvard.edu
wrote:
Does it print out anything else? An alternative is to use the command line stream (create your own fsgd file, run mris_preproc, smooth, mri_glmfit, mri_glmfit-sim) doug
On 05/27/2014 06:38 AM, Saloni Sharma wrote: I am attaching a screen shot of the error, if it helps!
On 26 May 2014 17:14, Saloni Sharma <sharmasa@tcd.ie mailto:sharmasa@tcd.ie> wrote:
yes exactly, if I click analyze without the gender it works fine. No thats okay, what do you need from me again?
On 26 May 2014 17:11, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
so if you click "analyze" without gender it works fine? Sorry, I missed that. I think you'll need to wait for Doug or Nick to reply, but you might send your qdec file and the group.levels files sorry BruceOn Mon, 26 May 2014, Saloni Sharma wrote:Hey Bruce,
Yes, that directory exists, as I said if I only choose
groups(high stressand low stress) as the discrete variables its runs fine and
analyses, itonly shows the error if I add more factors (like gender)
into the software.My subjects directory is set to export
SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/
and yes I have run recon-all-qcache on all my subjects.
Saloni
On 26 May 2014 16:58, Bruce Fischl
<fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:Hi Saloni Does that directory exist? What is your SUBJECTS_DIRset to? Andhave you run recon-all -qcache on all your subjects? cheers BruceOn Mon, 26 May 2014, Saloni Sharma wrote:Dear Freesurfers,
So I have followed all the instructions given on
your websitein order touse qdec. When i analyse the images only using a file
group.levels thatdefines the two groups I'm comparing the analysis
runs fineand gives meresults, but when I add gender, for instance, as a
discretefactor, it loadsthe data successfully but when I click analyse it
shows thefollowing error:Error in Analyze: Couldn't
openfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/
lh.thickness.fwhm10.fsaverage.mgh
Please guide me as to what is going wrong and what I
can do tofix it. Iwould appreciate a quick response as my thesis
submission isdue in twoweeks and I cannot proceed until this problem is sorted.
Thanks and regards, Saloni
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the
person to whomit is addressed. If you believe this e-mail was sent to you in
error and thee-mail contains patient information, please contact the Partners
ComplianceHelpLine at http://www.partners.org/complianceline . If the e-mail was
sent to youin error but does not contain patient information, please contact the
senderand properly dispose of the e-mail.
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Same error despite having run recon-qcache again.
On 28 May 2014 21:28, Saloni Sharma sharmasa@tcd.ie wrote:
Dear Nick,
I am certain of it because the analysis runs fine when I analyze it with just a discrete variable group.levels...the moment I add factor.levels as another variable along with groups it gives me the error. And if I remove this particular subject from the data table(this subject is the first on the data list) and try running it again it shows the same error for the next subject on the list.
I am attaching a screen shot of the said file existing as well.
However, I am also running the command you gave again as we speak, just to see if it works.
On 28 May 2014 20:48, Nick Schmansky, MGH nicks@nmr.mgh.harvard.eduwrote:
Saloni,
are you certain that you ran recon-qcache on subject 000054987500? the error message says that the file lh.thickness.fwhm10.fsaverage.mgh is missing, and this file is created by -qcache. i'd suggest running:
recon-all -s 000054987500 -qcache
then confirm that this file exists.
Nick
On Wed, 2014-05-28 at 01:21 +0100, Saloni wrote:
It prints out fine and gives results if I only use it to analyse two
groups(differentiated on stress levels) but if I add gender as a discrete variable or even as a continuous one along with the groups it shows this error.
Sent from my iPhone
On 27 May 2014, at 23:40, Douglas N Greve greve@nmr.mgh.harvard.edu
wrote:
Does it print out anything else? An alternative is to use the command line stream (create your own fsgd file, run mris_preproc, smooth, mri_glmfit, mri_glmfit-sim) doug
On 05/27/2014 06:38 AM, Saloni Sharma wrote: I am attaching a screen shot of the error, if it helps!
On 26 May 2014 17:14, Saloni Sharma <sharmasa@tcd.ie mailto:sharmasa@tcd.ie> wrote:
yes exactly, if I click analyze without the gender it works fine. No thats okay, what do you need from me again?
On 26 May 2014 17:11, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
so if you click "analyze" without gender it works fine? Sorry, I missed that. I think you'll need to wait for Doug or Nick to reply, but you might send your qdec file and the group.levels files sorry BruceOn Mon, 26 May 2014, Saloni Sharma wrote:Hey Bruce,
Yes, that directory exists, as I said if I only choose
groups(high stressand low stress) as the discrete variables its runs fine and
analyses, itonly shows the error if I add more factors (like gender)
into the software.My subjects directory is set to export
SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/
and yes I have run recon-all-qcache on all my subjects.
Saloni
On 26 May 2014 16:58, Bruce Fischl
<fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:Hi Saloni Does that directory exist? What is your SUBJECTS_DIRset to? Andhave you run recon-all -qcache on all your subjects? cheers Bruce> On Mon, 26 May 2014, Saloni Sharma wrote: > > Dear Freesurfers, > > So I have followed all the instructions given on
your websitein order to> use qdec. When i analyse the images only using a file group.levels that > defines the two groups I'm comparing the analysis
runs fineand gives me> results, but when I add gender, for instance, as a
discretefactor, it loads> the data successfully but when I click analyse it
shows thefollowing error:> > Error in Analyze: Couldn't
openfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/
lh.t> hickness.fwhm10.fsaverage.mgh > > Please guide me as to what is going wrong and what I
can do tofix it. I> would appreciate a quick response as my thesis
submission isdue in two> weeks and I cannot proceed until this problem is sorted. > > Thanks and regards, > Saloni _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the
person to whomit is addressed. If you believe this e-mail was sent to you in
error and thee-mail contains patient information, please contact the Partners
ComplianceHelpLine at http://www.partners.org/complianceline . If the e-mail was
sent to youin error but does not contain patient information, please contact the
senderand properly dispose of the e-mail.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
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Your subject name is wrong.
You are saying the subject name is: 000054987500
While it is actually: 000054987500_output
You should either change the name of the SUBJECT directory or change the subject id you are giving to mri_glmfit.
HTH D
On Wed, May 28, 2014 at 5:17 PM, Saloni Sharma sharmasa@tcd.ie wrote:
Same error despite having run recon-qcache again.
On 28 May 2014 21:28, Saloni Sharma sharmasa@tcd.ie wrote:
Dear Nick,
I am certain of it because the analysis runs fine when I analyze it with just a discrete variable group.levels...the moment I add factor.levels as another variable along with groups it gives me the error. And if I remove this particular subject from the data table(this subject is the first on the data list) and try running it again it shows the same error for the next subject on the list.
I am attaching a screen shot of the said file existing as well.
However, I am also running the command you gave again as we speak, just to see if it works.
On 28 May 2014 20:48, Nick Schmansky, MGH nicks@nmr.mgh.harvard.eduwrote:
Saloni,
are you certain that you ran recon-qcache on subject 000054987500? the error message says that the file lh.thickness.fwhm10.fsaverage.mgh is missing, and this file is created by -qcache. i'd suggest running:
recon-all -s 000054987500 -qcache
then confirm that this file exists.
Nick
On Wed, 2014-05-28 at 01:21 +0100, Saloni wrote:
It prints out fine and gives results if I only use it to analyse two
groups(differentiated on stress levels) but if I add gender as a discrete variable or even as a continuous one along with the groups it shows this error.
Sent from my iPhone
On 27 May 2014, at 23:40, Douglas N Greve greve@nmr.mgh.harvard.edu
wrote:
Does it print out anything else? An alternative is to use the command line stream (create your own fsgd file, run mris_preproc, smooth, mri_glmfit, mri_glmfit-sim) doug
On 05/27/2014 06:38 AM, Saloni Sharma wrote: I am attaching a screen shot of the error, if it helps!
On 26 May 2014 17:14, Saloni Sharma <sharmasa@tcd.ie mailto:sharmasa@tcd.ie> wrote:
yes exactly, if I click analyze without the gender it works fine. No thats okay, what do you need from me again?
On 26 May 2014 17:11, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
so if you click "analyze" without gender it works fine?Sorry,
I missed that. I think you'll need to wait for Doug or Nick to reply, but you might send your qdec file and the group.levels files sorry Bruce> On Mon, 26 May 2014, Saloni Sharma wrote: > > Hey Bruce, > > Yes, that directory exists, as I said if I only choose groups(high stress > and low stress) as the discrete variables its runs fine and analyses, it > only shows the error if I add more factors (like gender) into the software. > > My subjects directory is set to > export
SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/
> > and yes I have run recon-all-qcache on all my subjects. > > Saloni > > > On 26 May 2014 16:58, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: > Hi Saloni > > Does that directory exist? What is your SUBJECTS_DIR set to? And > have you > run recon-all -qcache on all your subjects? > > cheers > Bruce >> On Mon, 26 May 2014, Saloni Sharma wrote: >> >> Dear Freesurfers, >> >> So I have followed all the instructions given on your website > in order to >> use qdec. When i analyse the images only using a file > group.levels that >> defines the two groups I'm comparing the analysis runs fine > and gives me >> results, but when I add gender, for instance, as a discrete > factor, it loads >> the data successfully but when I click analyse it shows the > following error: >> >> Error in Analyze: Couldn't
openfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/
> lh.t >> hickness.fwhm10.fsaverage.mgh >> >> Please guide me as to what is going wrong and what I can do to > fix it. I >> would appreciate a quick response as my thesis submission is > due in two >> weeks and I cannot proceed until this problem is sorted. >> >> Thanks and regards, >> Saloni > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Daniel found your problem as he mentioned in his previous email (see below). Change the qdec table to have the name of the subject be 000054987500_output.
Also, I noticed that you have gender as a continuous variable. It should be discrete
-------- Original Message -------- Subject: Re: [Freesurfer] URGENT: Error in analyse Date: Wed, 28 May 2014 17:30:11 -0400 From: dgw dgwakeman@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu CC: nicks@nmr.mgh.harvard.edu
Your subject name is wrong.
You are saying the subject name is: 000054987500
While it is actually: 000054987500_output
You should either change the name of the SUBJECT directory or change the subject id you are giving to mri_glmfit.
HTH D
On 05/28/2014 05:17 PM, Saloni Sharma wrote:
Same error despite having run recon-qcache again.
On 28 May 2014 21:28, Saloni Sharma <sharmasa@tcd.ie mailto:sharmasa@tcd.ie> wrote:
Dear Nick, I am certain of it because the analysis runs fine when I analyze it with just a discrete variable group.levels...the moment I add factor.levels as another variable along with groups it gives me the error. And if I remove this particular subject from the data table(this subject is the first on the data list) and try running it again it shows the same error for the next subject on the list. I am attaching a screen shot of the said file existing as well. However, I am also running the command you gave again as we speak, just to see if it works. On 28 May 2014 20:48, Nick Schmansky, MGH <nicks@nmr.mgh.harvard.edu <mailto:nicks@nmr.mgh.harvard.edu>> wrote: Saloni, are you certain that you ran recon-qcache on subject 000054987500? the error message says that the file lh.thickness.fwhm10.fsaverage.mgh is missing, and this file is created by -qcache. i'd suggest running: recon-all -s 000054987500 -qcache then confirm that this file exists. Nick On Wed, 2014-05-28 at 01:21 +0100, Saloni wrote: > It prints out fine and gives results if I only use it to analyse two groups(differentiated on stress levels) but if I add gender as a discrete variable or even as a continuous one along with the groups it shows this error. > > Sent from my iPhone > > > On 27 May 2014, at 23:40, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > > > > Does it print out anything else? An alternative is to use the command > > line stream (create your own fsgd file, run mris_preproc, smooth, > > mri_glmfit, mri_glmfit-sim) > > doug > > > > > > > > > >> On 05/27/2014 06:38 AM, Saloni Sharma wrote: > >> I am attaching a screen shot of the error, if it helps! > >> > >> > >> On 26 May 2014 17:14, Saloni Sharma <sharmasa@tcd.ie <mailto:sharmasa@tcd.ie> > >> <mailto:sharmasa@tcd.ie <mailto:sharmasa@tcd.ie>>> wrote: > >> > >> yes exactly, if I click analyze without the gender it works fine. > >> No thats okay, what do you need from me again? > >> > >> > >> On 26 May 2014 17:11, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > >> > >> so if you click "analyze" without gender it works fine? Sorry, > >> I missed > >> that. I think you'll need to wait for Doug or Nick to reply, > >> but you might > >> send your qdec file and the group.levels files > >> > >> sorry > >> Bruce > >> > >>> On Mon, 26 May 2014, Saloni Sharma wrote: > >>> > >>> Hey Bruce, > >>> > >>> Yes, that directory exists, as I said if I only choose > >> groups(high stress > >>> and low stress) as the discrete variables its runs fine and > >> analyses, it > >>> only shows the error if I add more factors (like gender) > >> into the software. > >>> > >>> My subjects directory is set to > >>> export > >> SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/ > >>> > >>> and yes I have run recon-all-qcache on all my subjects. > >>> > >>> Saloni > >>> > >>> > >>> On 26 May 2014 16:58, Bruce Fischl > >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > >>> Hi Saloni > >>> > >>> Does that directory exist? What is your SUBJECTS_DIR > >> set to? And > >>> have you > >>> run recon-all -qcache on all your subjects? > >>> > >>> cheers > >>> Bruce > >>>> On Mon, 26 May 2014, Saloni Sharma wrote: > >>>> > >>>> Dear Freesurfers, > >>>> > >>>> So I have followed all the instructions given on > >> your website > >>> in order to > >>>> use qdec. When i analyse the images only using a file > >>> group.levels that > >>>> defines the two groups I'm comparing the analysis > >> runs fine > >>> and gives me > >>>> results, but when I add gender, for instance, as a > >> discrete > >>> factor, it loads > >>>> the data successfully but when I click analyse it > >> shows the > >>> following error: > >>>> > >>>> Error in Analyze: Couldn't > >> openfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/ > >>> lh.t > >>>> hickness.fwhm10.fsaverage.mgh > >>>> > >>>> Please guide me as to what is going wrong and what I > >> can do to > >>> fix it. I > >>>> would appreciate a quick response as my thesis > >> submission is > >>> due in two > >>>> weeks and I cannot proceed until this problem is sorted. > >>>> > >>>> Thanks and regards, > >>>> Saloni > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> The information in this e-mail is intended only for the > >> person to whom > >>> it is > >>> addressed. If you believe this e-mail was sent to you in > >> error and the > >>> e-mail > >>> contains patient information, please contact the Partners > >> Compliance > >>> HelpLine at > >>> http://www.partners.org/complianceline . If the e-mail was > >> sent to you > >>> in error > >>> but does not contain patient information, please contact the > >> sender > >>> and properly > >>> dispose of the e-mail. > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Yes! It worked! Thank you so much for all your help!
Best Regards, Saloni
On 28 May 2014 23:31, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Daniel found your problem as he mentioned in his previous email (see below). Change the qdec table to have the name of the subject be 000054987500_output.
Also, I noticed that you have gender as a continuous variable. It should be discrete
-------- Original Message -------- Subject: Re: [Freesurfer] URGENT: Error in analyse Date: Wed, 28 May 2014 17:30:11 -0400 From: dgw dgwakeman@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu CC: nicks@nmr.mgh.harvard.edu
Your subject name is wrong.
You are saying the subject name is: 000054987500
While it is actually: 000054987500_output
You should either change the name of the SUBJECT directory or change the subject id you are giving to mri_glmfit.
HTH D
On 05/28/2014 05:17 PM, Saloni Sharma wrote:
Same error despite having run recon-qcache again.
On 28 May 2014 21:28, Saloni Sharma <sharmasa@tcd.ie mailto:sharmasa@tcd.ie> wrote:
Dear Nick, I am certain of it because the analysis runs fine when I analyze it with just a discrete variable group.levels...the moment I add factor.levels as another variable along with groups it gives me the error. And if I remove this particular subject from the data table(this subject is the first on the data list) and try running it again it shows the same error for the next subject on the list. I am attaching a screen shot of the said file existing as well. However, I am also running the command you gave again as we speak, just to see if it works. On 28 May 2014 20:48, Nick Schmansky, MGH <nicks@nmr.mgh.harvard.edu <mailto:nicks@nmr.mgh.harvard.edu>>wrote:
Saloni, are you certain that you ran recon-qcache on subject 000054987500? the error message says that the file lh.thickness.fwhm10.fsaverage.mgh is missing, and this file is created by -qcache. i'd suggest running: recon-all -s 000054987500 -qcache then confirm that this file exists. Nick On Wed, 2014-05-28 at 01:21 +0100, Saloni wrote: > It prints out fine and gives results if I only use it to analyse two groups(differentiated on stress levels) but if I add gender as a discrete variable or even as a continuous one along with the groups it shows this error. > > Sent from my iPhone > > > On 27 May 2014, at 23:40, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > > > > Does it print out anything else? An alternative is to use the command > > line stream (create your own fsgd file, run mris_preproc, smooth, > > mri_glmfit, mri_glmfit-sim) > > doug > > > > > > > > > >> On 05/27/2014 06:38 AM, Saloni Sharma wrote: > >> I am attaching a screen shot of the error, if it helps! > >> > >> > >> On 26 May 2014 17:14, Saloni Sharma <sharmasa@tcd.ie <mailto:sharmasa@tcd.ie> > >> <mailto:sharmasa@tcd.ie <mailto:sharmasa@tcd.ie>>> wrote: > >> > >> yes exactly, if I click analyze without the gender it works fine. > >> No thats okay, what do you need from me again? > >> > >> > >> On 26 May 2014 17:11, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > >> > >> so if you click "analyze" without gender it works fine? Sorry, > >> I missed > >> that. I think you'll need to wait for Doug or Nick to reply, > >> but you might > >> send your qdec file and the group.levels files > >> > >> sorry > >> Bruce > >> > >>> On Mon, 26 May 2014, Saloni Sharma wrote: > >>> > >>> Hey Bruce, > >>> > >>> Yes, that directory exists, as I said if I only choose > >> groups(high stress > >>> and low stress) as the discrete variables its runs fine and > >> analyses, it > >>> only shows the error if I add more factors (like gender) > >> into the software. > >>> > >>> My subjects directory is set to > >>> export > >>SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/
> >>> > >>> and yes I have run recon-all-qcache on all my subjects. > >>> > >>> Saloni > >>> > >>> > >>> On 26 May 2014 16:58, Bruce Fischl > >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > >>> Hi Saloni > >>> > >>> Does that directory exist? What is your SUBJECTS_DIR > >> set to? And > >>> have you > >>> run recon-all -qcache on all your subjects? > >>> > >>> cheers > >>> Bruce > >>>> On Mon, 26 May 2014, Saloni Sharma wrote: > >>>> > >>>> Dear Freesurfers, > >>>> > >>>> So I have followed all the instructions given on > >> your website > >>> in order to > >>>> use qdec. When i analyse the images only using a file > >>> group.levels that > >>>> defines the two groups I'm comparing the analysis > >> runs fine > >>> and gives me > >>>> results, but when I add gender, for instance, as a > >> discrete > >>> factor, it loads > >>>> the data successfully but when I click analyse it > >> shows the > >>> following error: > >>>> > >>>> Error in Analyze: Couldn't > >>openfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/
> >>> lh.t > >>>> hickness.fwhm10.fsaverage.mgh > >>>> > >>>> Please guide me as to what is going wrong and what I > >> can do to > >>> fix it. I > >>>> would appreciate a quick response as my thesis > >> submission is > >>> due in two > >>>> weeks and I cannot proceed until this problem is sorted. > >>>> > >>>> Thanks and regards, > >>>> Saloni > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>> > >>> > >>> The information in this e-mail is intended only for the > >> person to whom > >>> it is > >>> addressed. If you believe this e-mail was sent to you in > >> error and the > >>> e-mail > >>> contains patient information, please contact the Partners > >> Compliance > >>> HelpLine at > >>> http://www.partners.org/complianceline . If the e-mail was > >> sent to you > >>> in error > >>> but does not contain patient information, please contactthe
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> >> > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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