Hi, I seem to have even less files:
Eran-Harels-MacBook-Pro:/applications/freesurfer] eiran% which $FREESURFER_HOME/bin/*.fsl /Applications/freesurfer/bin/epidewarp.fsl [Eran-Harels-MacBook-Pro:/applications/freesurfer] eiran% which $FREESURFER_HOME/bin/fsl* /Applications/freesurfer/bin/fsl_label2voxel
Eiran
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschwind@gmail.com] Sent: Thursday, April 03, 2014 3:43 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question
Hi Eiran and Doug,
I do not have bet.fsl neither (c.f. previous mail with the list of what I had).
It seems that there is quite some more missing in the mac build...
This is what I find on my ubuntu installation freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
$ ls $FREESURFER_HOME/bin/*.fsl /usr/local/freesurfer/bin/bet.fsl /usr/local/freesurfer/bin/epidewarp.fsl /usr/local/freesurfer/bin/flirt.fsl /usr/local/freesurfer/bin/fscalc.fsl /usr/local/freesurfer/bin/fslmaths.fsl /usr/local/freesurfer/bin/fslorient.fsl /usr/local/freesurfer/bin/fslswapdim.fsl /usr/local/freesurfer/bin/mri_motion_correct.fsl /usr/local/freesurfer/bin/slicetimer.fsl
$ ls $FREESURFER_HOME/bin/fsl* /usr/local/freesurfer/bin/fsl_label2voxel /usr/local/freesurfer/bin/fslmaths.fsl /usr/local/freesurfer/bin/fslorient.fsl /usr/local/freesurfer/bin/fslregister /usr/local/freesurfer/bin/fsl_rigid_register /usr/local/freesurfer/bin/fsl_sub_mgh /usr/local/freesurfer/bin/fslswapdim.fsl
And this is what I have on my Mac OSX installation (freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0)
$ which $FREESURFER_HOME/bin/fsl* /Applications/freesurfer/bin/fsl_label2voxel /Applications/freesurfer/bin/fsl_rigid_register /Applications/freesurfer/bin/fsl_sub_mgh /Applications/freesurfer/bin/fslregister
$ which $FREESURFER_HOME/bin/*.fsl /Applications/freesurfer/bin/epidewarp.fsl /Applications/freesurfer/bin/fscalc.fsl /Applications/freesurfer/bin/mri_motion_correct.fsl
Best, Markus
2014-04-03 13:35 GMT+02:00 Eiran Harel <eiranh@tlvmc.gov.ilmailto:eiranh@tlvmc.gov.il>: Hi Doug, I changed the file permissions to be executable and it passed this stage. It then gets stuck when looking for bet.fsl:
# ---------- Using FSL's BET to Extract Brain------------------ # /applications/freesurfer/BSMT_project/bsmt103/bold bet.fsl /tmp/mkbrainmask_76128/in.nii /tmp/mkbrainmask_76128/brain -m -f 0.1 bet.fsl: Command not found. ERROR: bet failed
Was there something wrong in the insatallation that it is missing those files? Thanks! Eiran
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 5:21 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] preprocessing question
a couple of thiings to check: make sure it is exectuable and make sure that you rehash your path. Make sure that if you type fslmaths.fsl that it runs something
On 04/02/2014 03:23 AM, Eiran Harel wrote:
Thanks Doug, i downloaded it and now the file exists:
$FREESURFER_HOME/bin/fslmaths.fsl
Unfortuantely it is still not running and gives the same error when running preproc-sess:
mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 ERROR: cannot find either fslmaths for avwmaths
How can i proceed? Thanks, Eiran ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 12:41 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] preprocessing question
thanks, it must be something in our distribution script affecting mac
On 04/01/2014 05:13 PM, Markus Gschwind wrote:
Thanks Doug,
I notice that on my Mac build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
...I don't have fslmaths.fsl neither. There are only
$ which $FREESURFER_HOME/bin/fsl* /Applications/freesurfer/bin/fsl_label2voxel /Applications/freesurfer/bin/fsl_rigid_register /Applications/freesurfer/bin/fsl_sub_mgh /Applications/freesurfer/bin/fslregister $ which $FREESURFER_HOME/bin/*.fsl /Applications/freesurfer/bin/epidewarp.fsl /Applications/freesurfer/bin/fscalc.fsl /Applications/freesurfer/bin/mri_motion_correct.fsl(I never executed the above mentioned process of Eiran thoug...)
Best, Markus
2014-04-01 18:36 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu>>:
That is weird. You can get a copy from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac copy it to $FREESURFER_HOME/bin/fslmaths.fsl On 04/01/2014 12:25 PM, Eiran Harel wrote: > Hi Doug, > No, it does not exist. > What should i do? > Thanks, > Eiran > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> [freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>>] > Sent: Tuesday, April 01, 2014 7:16 PM > To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] preprocessing question > > does $FREESURFER_HOME/bin/fslmaths.fsl exist? > > On 04/01/2014 03:59 AM, Eiran Harel wrote: >> Dear freesurfers, >> I have installed freesurfer and fsl on my Mac: >> * >> * >> *-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------* >> *Setting up environment for FreeSurfer/FS-FAST (and FSL)* >> *FREESURFER_HOME /Applications/freesurfer* >> *FSFAST_HOME /Applications/freesurfer/fsfast* >> *FSF_OUTPUT_FORMAT nii.gz* >> *SUBJECTS_DIR /Applications/freesurfer/subjects* >> *MNI_DIR /Applications/freesurfer/mni* >> *FSL_DIR /usr/local/fsl* >> >> I am trying to run Preproc-sess command: >> >> *preproc-sess -s bsmt102 -surface fsaverage lhrh -mni305 -fwhm 5 -fsd >> bold -stc odd -per-run -force* >> >> and get this error: >> >> *mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 >> -ndil 1 -nerode 0* >> *ERROR: cannot find either fslmaths for avwmaths* >> * >> * >> Any suggestions? >> Thanks! >> Eiran >> >> >> >> >> <http://www.tasmc.org.il/be-well/Pages/default.aspx> >> <https://www.facebook.com/ichilov.medical> >> <http://twitter.com/tasmc1> <http://www.youtube.com/tasmc1> >> <http://www.tasmc.org.il/sites/en/Pages/default.aspx> >> >> >> >> >> _______________________________________________ >> 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 > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358<tel:617-724-2358> <tel:617-724-2358<tel:617-724-2358>> > Fax: 617-726-7422<tel:617-726-7422> <tel:617-726-7422<tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://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> <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> <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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358<tel:617-724-2358> <tel:617-724-2358<tel:617-724-2358>> Fax: 617-726-7422<tel:617-726-7422> <tel:617-726-7422<tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://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> <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> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358tel:617-724-2358 Fax: 617-726-7422tel:617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358tel:617-724-2358 Fax: 617-726-7422tel:617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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