Dear All, I was wondering if anyone knows of a step-by-step guide on how to do retinotopic analysis with freesurfer.
Thanks. Michelle
I don't have a formal manual yet (working on it). Below are a list of steps that you need to run. The version 5 retinotopy stream is now integrated with the rest of FSFAST, which is documented here: http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt
doug
1. Create retinotopy paradigm file in each run directory, eg, session/bold/001/rtopy.par session/bold/002/rtopy.par etc
This text file identifies the data in the directory in terms of the stimulus type (polar or eccen) and the direction (pos or neg). Its contents should look somethign like:
stimtype polar direction pos
2. Run preprocessing
preproc-sess -surface self lhrh -fwhm 5
3. Create analysis (30 sec period, 'rtopy.par' is the name of the paradigm file from above):
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ -retinotopy 30 -paradigm rtopy.par
4. Run analysis
selxavg3-sess -a rtopy.self.lh -sf ... selxavg3-sess -a rtopy.self.rh -sf ... fieldsign-sess -a rtopy.self.lh -occip -sf ... fieldsign-sess -a rtopy.self.rh -occip -sf ...
5. View results a. Significance maps: tksurfer-sess -a rtopy.self.lh -s sessid b. Display raw angle tksurfer-sess -a rtopy.self.lh -s sessid -map angle c. Display angle masked by by sig tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked d. Display field sign tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign
Michelle Umali wrote:
Dear All, I was wondering if anyone knows of a step-by-step guide on how to do retinotopic analysis with freesurfer.
Thanks. Michelle _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, Sorry for the dumb beginner question, but to view the results projected onto their own anatomy, do I have to do anything special to their high res structural scan(like do a recon-all) ?
Thanks. Michelle
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
I don't have a formal manual yet (working on it). Below are a list of steps that you need to run. The version 5 retinotopy stream is now integrated with the rest of FSFAST, which is documented here: http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt
doug
- Create retinotopy paradigm file in each run directory, eg, session/bold/001/rtopy.par session/bold/002/rtopy.par etc
This text file identifies the data in the directory in terms of the stimulus type (polar or eccen) and the direction (pos or neg). Its contents should look somethign like:
stimtype polar direction pos
- Run preprocessing
preproc-sess -surface self lhrh -fwhm 5
- Create analysis (30 sec period, 'rtopy.par' is the name of the
paradigm file from above):
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ -retinotopy 30 -paradigm rtopy.par
- Run analysis
selxavg3-sess -a rtopy.self.lh -sf ... selxavg3-sess -a rtopy.self.rh -sf ... fieldsign-sess -a rtopy.self.lh -occip -sf ... fieldsign-sess -a rtopy.self.rh -occip -sf ...
- View results
a. Significance maps: tksurfer-sess -a rtopy.self.lh -s sessid b. Display raw angle tksurfer-sess -a rtopy.self.lh -s sessid -map angle c. Display angle masked by by sig tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked d. Display field sign tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign
Michelle Umali wrote:
Dear All, I was wondering if anyone knows of a step-by-step guide on how to do retinotopic analysis with freesurfer.
Thanks. Michelle _______________________________________________ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Yes, you need to run recon-all in order to run the FSFAST analysis.
doug
Michelle Umali wrote:
Hi Doug, Sorry for the dumb beginner question, but to view the results projected onto their own anatomy, do I have to do anything special to their high res structural scan(like do a recon-all) ?
Thanks. Michelle
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
I don't have a formal manual yet (working on it). Below are a list of steps that you need to run. The version 5 retinotopy stream is now integrated with the rest of FSFAST, which is documented here: http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt
doug
- Create retinotopy paradigm file in each run directory, eg, session/bold/001/rtopy.par session/bold/002/rtopy.par etc
This text file identifies the data in the directory in terms of the stimulus type (polar or eccen) and the direction (pos or neg). Its contents should look somethign like:
stimtype polar direction pos
- Run preprocessing
preproc-sess -surface self lhrh -fwhm 5
- Create analysis (30 sec period, 'rtopy.par' is the name of the
paradigm file from above):
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ -retinotopy 30 -paradigm rtopy.par
- Run analysis
selxavg3-sess -a rtopy.self.lh -sf ... selxavg3-sess -a rtopy.self.rh -sf ... fieldsign-sess -a rtopy.self.lh -occip -sf ... fieldsign-sess -a rtopy.self.rh -occip -sf ...
- View results
a. Significance maps: tksurfer-sess -a rtopy.self.lh -s sessid b. Display raw angle tksurfer-sess -a rtopy.self.lh -s sessid -map angle c. Display angle masked by by sig tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked d. Display field sign tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign
Michelle Umali wrote:
Dear All, I was wondering if anyone knows of a step-by-step guide on how to do retinotopic analysis with freesurfer.
Thanks. Michelle _______________________________________________ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Hi Doug, When you say retinotopy 30, where 30 is the 30 second period.
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par
Does period mean duration for a cycle or for the whole run?
Thanks. Michelle
ing Douglas N Greve greve@nmr.mgh.harvard.edu:
I don't have a formal manual yet (working on it). Below are a list of steps that you need to run. The version 5 retinotopy stream is now integrated with the rest of FSFAST, which is documented here: http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt
doug
- Create retinotopy paradigm file in each run directory, eg, session/bold/001/rtopy.par session/bold/002/rtopy.par etc
This text file identifies the data in the directory in terms of the stimulus type (polar or eccen) and the direction (pos or neg). Its contents should look somethign like:
stimtype polar direction pos
- Run preprocessing
preproc-sess -surface self lhrh -fwhm 5
- Create analysis (30 sec period, 'rtopy.par' is the name of the
paradigm file from above):
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ -retinotopy 30 -paradigm rtopy.par
- Run analysis
selxavg3-sess -a rtopy.self.lh -sf ... selxavg3-sess -a rtopy.self.rh -sf ... fieldsign-sess -a rtopy.self.lh -occip -sf ... fieldsign-sess -a rtopy.self.rh -occip -sf ...
- View results
a. Significance maps: tksurfer-sess -a rtopy.self.lh -s sessid b. Display raw angle tksurfer-sess -a rtopy.self.lh -s sessid -map angle c. Display angle masked by by sig tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked d. Display field sign tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign
Michelle Umali wrote:
Dear All, I was wondering if anyone knows of a step-by-step guide on how to do retinotopic analysis with freesurfer.
Thanks. Michelle _______________________________________________ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
For a cycle. So for the time it take the wedge to go all the way around or for the ring to start from center and return to center.
doug
Michelle Umali wrote:
Hi Doug, When you say retinotopy 30, where 30 is the 30 second period.
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par
Does period mean duration for a cycle or for the whole run?
Thanks. Michelle
ing Douglas N Greve greve@nmr.mgh.harvard.edu:
I don't have a formal manual yet (working on it). Below are a list of steps that you need to run. The version 5 retinotopy stream is now integrated with the rest of FSFAST, which is documented here: http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt
doug
- Create retinotopy paradigm file in each run directory, eg, session/bold/001/rtopy.par session/bold/002/rtopy.par etc
This text file identifies the data in the directory in terms of the stimulus type (polar or eccen) and the direction (pos or neg). Its contents should look somethign like:
stimtype polar direction pos
- Run preprocessing
preproc-sess -surface self lhrh -fwhm 5
- Create analysis (30 sec period, 'rtopy.par' is the name of the
paradigm file from above):
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ -retinotopy 30 -paradigm rtopy.par
- Run analysis
selxavg3-sess -a rtopy.self.lh -sf ... selxavg3-sess -a rtopy.self.rh -sf ... fieldsign-sess -a rtopy.self.lh -occip -sf ... fieldsign-sess -a rtopy.self.rh -occip -sf ...
- View results
a. Significance maps: tksurfer-sess -a rtopy.self.lh -s sessid b. Display raw angle tksurfer-sess -a rtopy.self.lh -s sessid -map angle c. Display angle masked by by sig tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked d. Display field sign tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign
Michelle Umali wrote:
Dear All, I was wondering if anyone knows of a step-by-step guide on how to do retinotopic analysis with freesurfer.
Thanks. Michelle _______________________________________________ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Dear Freesurfers, I am still struggling with the retinotopy analysis. Whenever I try to run preproc-sess, I get this message:
Session: /home/fsl/structural/LD08 ---------------- Tue Apr 5 07:22:28 BST 2011 is not in SUBJECTS_DIR SUBJECTS_DIR is /home/fsl/structural
I put the retinotopic and structural data into the structural directory. In addition, I have the subjectname file that contains LD08 in this case.
Any help would be most appreciated. I am attaching the output, in case it is helpful.
Thanks. Michelle
ing Douglas N Greve greve@nmr.mgh.harvard.edu:
I don't have a formal manual yet (working on it). Below are a list of steps that you need to run. The version 5 retinotopy stream is now integrated with the rest of FSFAST, which is documented here: http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt
doug
- Create retinotopy paradigm file in each run directory, eg, session/bold/001/rtopy.par session/bold/002/rtopy.par etc
This text file identifies the data in the directory in terms of the stimulus type (polar or eccen) and the direction (pos or neg). Its contents should look somethign like:
stimtype polar direction pos
- Run preprocessing
preproc-sess -surface self lhrh -fwhm 5
- Create analysis (30 sec period, 'rtopy.par' is the name of the
paradigm file from above):
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ -retinotopy 30 -paradigm rtopy.par
- Run analysis
selxavg3-sess -a rtopy.self.lh -sf ... selxavg3-sess -a rtopy.self.rh -sf ... fieldsign-sess -a rtopy.self.lh -occip -sf ... fieldsign-sess -a rtopy.self.rh -occip -sf ...
- View results
a. Significance maps: tksurfer-sess -a rtopy.self.lh -s sessid b. Display raw angle tksurfer-sess -a rtopy.self.lh -s sessid -map angle c. Display angle masked by by sig tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked d. Display field sign tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign
Make sure that your subjectname file has the name of the FreeSurfer subject folder as found in $SUBJECTS_DIR (it looks like it is empty). You don't need the retinotopy data in the $SUBJECTS_DIR. doug
Michelle Umali wrote:
Dear Freesurfers, I am still struggling with the retinotopy analysis. Whenever I try to run preproc-sess, I get this message:
Session: /home/fsl/structural/LD08 ---------------- Tue Apr 5 07:22:28 BST 2011 is not in SUBJECTS_DIR SUBJECTS_DIR is /home/fsl/structural
I put the retinotopic and structural data into the structural directory. In addition, I have the subjectname file that contains LD08 in this case.
Any help would be most appreciated. I am attaching the output, in case it is helpful.
Thanks. Michelle
ing Douglas N Greve greve@nmr.mgh.harvard.edu:
I don't have a formal manual yet (working on it). Below are a list of steps that you need to run. The version 5 retinotopy stream is now integrated with the rest of FSFAST, which is documented here: http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt
doug
- Create retinotopy paradigm file in each run directory, eg, session/bold/001/rtopy.par session/bold/002/rtopy.par etc
This text file identifies the data in the directory in terms of the stimulus type (polar or eccen) and the direction (pos or neg). Its contents should look somethign like:
stimtype polar direction pos
- Run preprocessing
preproc-sess -surface self lhrh -fwhm 5
- Create analysis (30 sec period, 'rtopy.par' is the name of the
paradigm file from above):
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ -retinotopy 30 -paradigm rtopy.par
- Run analysis
selxavg3-sess -a rtopy.self.lh -sf ... selxavg3-sess -a rtopy.self.rh -sf ... fieldsign-sess -a rtopy.self.lh -occip -sf ... fieldsign-sess -a rtopy.self.rh -occip -sf ...
- View results
a. Significance maps: tksurfer-sess -a rtopy.self.lh -s sessid b. Display raw angle tksurfer-sess -a rtopy.self.lh -s sessid -map angle c. Display angle masked by by sig tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked d. Display field sign tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign
Hi Doug, Does the $SUBJECTS_DIR folder have to be where the FreeSurfer program is? I had done this:
setenv SUBJECTS_DIR /home/fsl/structural So this SUBJECTS_DIR is not located where FreeSurfer is.
Is the following the exact correct path: FreeSurfer/$SUBJECTS_DIR/LD08/subjectname where LD08 is the file subjectname says LD08 and freesurfer must be capitalized as FreeSurfer?
and all the retinotopy data can be in: /home/fsl/structural/bold
and recon-all subfolders and data in /home/fsl/structural
Sorry for such a basic question.
Thanks. Michelle
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Make sure that your subjectname file has the name of the FreeSurfer subject folder as found in $SUBJECTS_DIR (it looks like it is empty). You don't need the retinotopy data in the $SUBJECTS_DIR. doug
Michelle Umali wrote:
Dear Freesurfers, I am still struggling with the retinotopy analysis. Whenever I try to run preproc-sess, I get this message:
Session: /home/fsl/structural/LD08 ---------------- Tue Apr 5 07:22:28 BST 2011 is not in SUBJECTS_DIR SUBJECTS_DIR is /home/fsl/structural
I put the retinotopic and structural data into the structural directory. In addition, I have the subjectname file that contains LD08 in this case.
Any help would be most appreciated. I am attaching the output, in case it is helpful.
Thanks. Michelle
Hi Michelle,
the SUBJECTS_DIR is an environment variable that you have to set prior to running the anatomical analysis (disregarding the functional analysis for a moment). Before running the functional analysis, you must run recon-all on the anatomical data, eg
recon-all -all -subject LD08-anat -i anatomical.dicom
this will create a folder in $SUBJECTS_DIR called LD08-anat. If you have not done this, you should do this first. Look at the wiki for how to run the anatomical analysis.
Once this is done, you should unpack your functional data (looks like you might have done this already). In the session directory, create a text file called "subjectname". Put the subject name (ie, LD08-anat) into the subjectname file.
doug
On 4/5/11 2:15 PM, Michelle Umali wrote:
Hi Doug, Does the $SUBJECTS_DIR folder have to be where the FreeSurfer program is? I had done this:
setenv SUBJECTS_DIR /home/fsl/structural So this SUBJECTS_DIR is not located where FreeSurfer is.
Is the following the exact correct path: FreeSurfer/$SUBJECTS_DIR/LD08/subjectname where LD08 is the file subjectname says LD08 and freesurfer must be capitalized as FreeSurfer?
and all the retinotopy data can be in: /home/fsl/structural/bold
and recon-all subfolders and data in /home/fsl/structural
Sorry for such a basic question.
Thanks. Michelle
Quoting Douglas N Grevegreve@nmr.mgh.harvard.edu:
Make sure that your subjectname file has the name of the FreeSurfer subject folder as found in $SUBJECTS_DIR (it looks like it is empty). You don't need the retinotopy data in the $SUBJECTS_DIR. doug
Michelle Umali wrote:
Dear Freesurfers, I am still struggling with the retinotopy analysis. Whenever I try to run preproc-sess, I get this message:
Session: /home/fsl/structural/LD08 ---------------- Tue Apr 5 07:22:28 BST 2011 is not in SUBJECTS_DIR SUBJECTS_DIR is /home/fsl/structural
I put the retinotopic and structural data into the structural directory. In addition, I have the subjectname file that contains LD08 in this case.
Any help would be most appreciated. I am attaching the output, in case it is helpful.
Thanks. Michelle
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I've run recon-all -all. I ended up inputing an .mgz file converted from a .nii file that was converted from a .dicom. Was needed info lost somewhere along the way?
Anyway, I thought I ran recon-all -all LD08 (wasn't LD08-anat, does one need -anat?)successfully, because it generated the following folders: bem, label, mri, scripts, src, stats, surf, tmp, touch, trash. And the bem, src, and trash folders are empty, but the others are full of files.
Eek.
-Michelle
Hi Michelle,
the SUBJECTS_DIR is an environment variable that you have to set prior to running the anatomical analysis (disregarding the functional analysis for a moment). Before running the functional analysis, you must run recon-all on the anatomical data, eg
recon-all -all -subject LD08-anat -i anatomical.dicom
this will create a folder in $SUBJECTS_DIR called LD08-anat. If you have not done this, you should do this first. Look at the wiki for how to run the anatomical analysis.
Once this is done, you should unpack your functional data (looks like you might have done this already). In the session directory, create a text file called "subjectname". Put the subject name (ie, LD08-anat) into the subjectname file.
doug
On 4/5/11 2:15 PM, Michelle Umali wrote:
Hi Doug, Does the $SUBJECTS_DIR folder have to be where the FreeSurfer program is? I had done this:
setenv SUBJECTS_DIR /home/fsl/structural So this SUBJECTS_DIR is not located where FreeSurfer is.
Is the following the exact correct path: FreeSurfer/$SUBJECTS_DIR/LD08/subjectname where LD08 is the file subjectname says LD08 and freesurfer must be capitalized as FreeSurfer?
and all the retinotopy data can be in: /home/fsl/structural/bold
and recon-all subfolders and data in /home/fsl/structural
Sorry for such a basic question.
Thanks. Michelle
You should check that anatomical analysis and make sure that it is correct. Once that is done, make sure that the subjectname in the subjectname file is correct, then preproc-sess should run.
doug
Michelle Umali wrote:
Hi Doug,
I've run recon-all -all. I ended up inputing an .mgz file converted from a .nii file that was converted from a .dicom. Was needed info lost somewhere along the way?
Anyway, I thought I ran recon-all -all LD08 (wasn't LD08-anat, does one need -anat?)successfully, because it generated the following folders: bem, label, mri, scripts, src, stats, surf, tmp, touch, trash. And the bem, src, and trash folders are empty, but the others are full of files.
Eek.
-Michelle
Hi Michelle,
the SUBJECTS_DIR is an environment variable that you have to set prior to running the anatomical analysis (disregarding the functional analysis for a moment). Before running the functional analysis, you must run recon-all on the anatomical data, eg
recon-all -all -subject LD08-anat -i anatomical.dicom
this will create a folder in $SUBJECTS_DIR called LD08-anat. If you have not done this, you should do this first. Look at the wiki for how to run the anatomical analysis.
Once this is done, you should unpack your functional data (looks like you might have done this already). In the session directory, create a text file called "subjectname". Put the subject name (ie, LD08-anat) into the subjectname file.
doug
On 4/5/11 2:15 PM, Michelle Umali wrote:
Hi Doug, Does the $SUBJECTS_DIR folder have to be where the FreeSurfer program is? I had done this:
setenv SUBJECTS_DIR /home/fsl/structural So this SUBJECTS_DIR is not located where FreeSurfer is.
Is the following the exact correct path: FreeSurfer/$SUBJECTS_DIR/LD08/subjectname where LD08 is the file subjectname says LD08 and freesurfer must be capitalized as FreeSurfer?
and all the retinotopy data can be in: /home/fsl/structural/bold
and recon-all subfolders and data in /home/fsl/structural
Sorry for such a basic question.
Thanks. Michelle
freesurfer@nmr.mgh.harvard.edu