Hi Julia

that seems unlikely. What happens when you type:

ls $FREESURFER_HOME/bin/mris_preproc

cheers Bruce On Tue, 5 Jun 2012, Richter, Julia wrote:

Could it be that the mris_preproc and the mri_glmfit file are missing in my freesurfer package? If so, can anybody send them to me?

Thank you very much,

Julia ________________________________ Von: Richter, Julia Gesendet: Dienstag, 5. Juni 2012 10:11 Bis: freesurfer@nmr.mgh.harvard.edu Betreff: mris_preproc

Dear FreeSurfer experts,

I am trying to run mris_preproc after caching my data. As command lines, I am typing:

mris_preproc --fsgd file.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.allpatients.thickness10.mgh

Everytime I am trying to run these commands, it tells me that it does not know the command mris_preproc. I have no clue what is going on here. Any suggestions?

Thanks for your help,

best Julia

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

okay, how about:

which mris_preproc

and just

mris_preproc

On Tue, 5 Jun 2012, Richter, Julia wrote:

after typing your command in my terminal window, it appears:

/usr/local/freesurfer/bin/mris_preproc ________________________________________ Von: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Dienstag, 5. Juni 2012 15:05 Bis: Richter, Julia Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mris_preproc

Hi Julia

that seems unlikely. What happens when you type:

ls $FREESURFER_HOME/bin/mris_preproc

cheers Bruce On Tue, 5 Jun 2012, Richter, Julia wrote:

...

Could it be that the mris_preproc and the mri_glmfit file are missing in my freesurfer package? If so, can anybody send them to me?

Thank you very much,

Julia ________________________________ Von: Richter, Julia Gesendet: Dienstag, 5. Juni 2012 10:11 Bis: freesurfer@nmr.mgh.harvard.edu Betreff: mris_preproc

Dear FreeSurfer experts,

I am trying to run mris_preproc after caching my data. As command lines, I am typing:

mris_preproc --fsgd file.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.allpatients.thickness10.mgh

Everytime I am trying to run these commands, it tells me that it does not know the command mris_preproc. I have no clue what is going on here. Any suggestions?

Thanks for your help,

best Julia

---

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 your path must be wrong then. Are you sourcing $FREESURFER_HOME/FreeSurferEnv.csh? That is, in your .login or .cshrc or whatever gets run at startup do you do:

source $FREESURFER_HOME/FreeSurferEnv.csh

try running that at the command line and see if it finds mris_preproc afterwards.

cheers Bruce

On Tue, 5 Jun 2012, Richter, Julia wrote:

nothing happens when typing "which mris_prepoc", command not found when typing only "mris_preproc" ________________________________________ Von: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Dienstag, 5. Juni 2012 15:25 Bis: Richter, Julia Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW: [Freesurfer] mris_preproc

okay, how about:

which mris_preproc

and just

mris_preproc

On Tue, 5 Jun 2012, Richter, Julia wrote:

...

after typing your command in my terminal window, it appears:

/usr/local/freesurfer/bin/mris_preproc ________________________________________ Von: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Dienstag, 5. Juni 2012 15:05 Bis: Richter, Julia Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mris_preproc

Hi Julia

that seems unlikely. What happens when you type:

ls $FREESURFER_HOME/bin/mris_preproc

cheers Bruce On Tue, 5 Jun 2012, Richter, Julia wrote:

...

Could it be that the mris_preproc and the mri_glmfit file are missing in my freesurfer package? If so, can anybody send them to me?

Thank you very much,

Julia ________________________________ Von: Richter, Julia Gesendet: Dienstag, 5. Juni 2012 10:11 Bis: freesurfer@nmr.mgh.harvard.edu Betreff: mris_preproc

Dear FreeSurfer experts,

I am trying to run mris_preproc after caching my data. As command lines, I am typing:

mris_preproc --fsgd file.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.allpatients.thickness10.mgh

Everytime I am trying to run these commands, it tells me that it does not know the command mris_preproc. I have no clue what is going on here. Any suggestions?

Thanks for your help,

best Julia

---

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.