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

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

-- 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

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

-- 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.

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

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

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

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