Re: [Freesurfer] preprocessing question
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 5:21 PM To: 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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 12:41 AM To: 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 gr...@nmr.mgh.harvard.edu mailto:gr...@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-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:16 PM To: 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 https
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 eir...@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-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [ gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 5:21 PM To: 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-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [ gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 12:41 AM To: 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 gr...@nmr.mgh.harvard.edu mailto:gr...@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-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:16 PM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] preprocessing question
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@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 eir...@tlvmc.gov.ilmailto:eir...@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-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edumailto:gr...@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-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edumailto:gr...@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 gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Re: [Freesurfer] preprocessing question
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 12:41 AM To: 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 gr...@nmr.mgh.harvard.edu mailto:gr...@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-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:16 PM To: 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@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 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
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 12:41 AM To: 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 gr...@nmr.mgh.harvard.edu mailto:gr...@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-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:16 PM To: 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@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
Re: [Freesurfer] preprocessing question
Hi! Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/) What happens if you type in your terminal fslmaths ? Best, Markus 2014-04-01 9:59 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il: 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 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 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.
Re: [Freesurfer] preprocessing question
Hi, Although there are matlab utils as part of FSL in $FSL_DIR/etc/matlab that can be used in FSL, I think it is not necessary to have matlab working for FSL to work. There are many more matlab utils in Freesurfer ($FREESURFER_HOME/matlab). The error message tells you that freesurfer doesn't find fslmaths in the fsl directory... Can you post here the exact result of more $FSL_DIR/etc/fslversion and echo $FSLDIR #(without the _ between FSL and DIR!) Best, Markus 2014-04-01 12:13 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il: Hi Markus, Thanks, it's is in FSL_DIR /usr/local/fsl. Is MATLAB necessary to run FSL? EIran *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ markus.gschw...@gmail.com] *Sent:* Tuesday, April 01, 2014 12:55 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] preprocessing question Hi, what does it say when you type which fsl which fslmath ? It mud be the same thing as FSL_DIR /usr/local/fsl It is possible that the FSL_DIR specified in the freesurfersetup is not the good one... Best, Markus 2014-04-01 10:25 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il: Hi Markus, Thanks, i did install fsl and when i type fslmaths it gives me the help for that command. Any other suggestions? Eiran -- *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ markus.gschw...@gmail.com] *Sent:* Tuesday, April 01, 2014 11:11 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] preprocessing question Hi! Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/) What happens if you type in your terminal fslmaths ? Best, Markus 2014-04-01 9:59 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il: 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 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 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom
Re: [Freesurfer] preprocessing question
Hi Markus, [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% more $FSL_DIR/etc/fslversion 5.0.6 [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% echo $FSLDIR /usr/local/fsl Thanks! Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.com] Sent: Tuesday, April 01, 2014 2:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question Hi, Although there are matlab utils as part of FSL in $FSL_DIR/etc/matlab that can be used in FSL, I think it is not necessary to have matlab working for FSL to work. There are many more matlab utils in Freesurfer ($FREESURFER_HOME/matlab). The error message tells you that freesurfer doesn't find fslmaths in the fsl directory... Can you post here the exact result of more $FSL_DIR/etc/fslversion and echo $FSLDIR #(without the _ between FSL and DIR!) Best, Markus 2014-04-01 12:13 GMT+02:00 Eiran Harel eir...@tlvmc.gov.ilmailto:eir...@tlvmc.gov.il: Hi Markus, Thanks, it's is in FSL_DIR /usr/local/fsl. Is MATLAB necessary to run FSL? EIran From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.commailto:markus.gschw...@gmail.com] Sent: Tuesday, April 01, 2014 12:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question Hi, what does it say when you type which fsl which fslmath ? It mud be the same thing as FSL_DIR /usr/local/fsl It is possible that the FSL_DIR specified in the freesurfersetup is not the good one… Best, Markus 2014-04-01 10:25 GMT+02:00 Eiran Harel eir...@tlvmc.gov.ilmailto:eir...@tlvmc.gov.il: Hi Markus, Thanks, i did install fsl and when i type fslmaths it gives me the help for that command. Any other suggestions? Eiran From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.commailto:markus.gschw...@gmail.com] Sent: Tuesday, April 01, 2014 11:11 AM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question Hi! Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/) What happens if you type in your terminal fslmaths ? Best, Markus 2014-04-01 9:59 GMT+02:00 Eiran Harel eir...@tlvmc.gov.ilmailto:eir...@tlvmc.gov.il: 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/DocLib/SIGN/sign_smallHE_01.jpg]http://www.tasmc.org.il/be-well/Pages/default.aspx [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_02.jpg] https://www.facebook.com/ichilov.medical [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_03.jpg] http://twitter.com/tasmc1 [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_04.jpg] http://www.youtube.com/tasmc1 [http://www.tasmc.org.il/DocLib/SIGN/sign_smallEN_05.jpg] http://www.tasmc.org.il/sites/en/Pages/default.aspx ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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
Re: [Freesurfer] preprocessing question
Well, Eiran, That seems all fine. Maybe Bruce or Doug can jump in and help? Sorry! Markus 2014-04-01 15:25 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il: Hi Markus, [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% more $FSL_DIR/etc/fslversion 5.0.6 [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% echo $FSLDIR /usr/local/fsl Thanks! Eiran *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ markus.gschw...@gmail.com] *Sent:* Tuesday, April 01, 2014 2:48 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] preprocessing question Hi, Although there are matlab utils as part of FSL in $FSL_DIR/etc/matlab that can be used in FSL, I think it is not necessary to have matlab working for FSL to work. There are many more matlab utils in Freesurfer ($FREESURFER_HOME/matlab). The error message tells you that freesurfer doesn't find fslmaths in the fsl directory... Can you post here the exact result of more $FSL_DIR/etc/fslversion and echo $FSLDIR #(without the _ between FSL and DIR!) Best, Markus 2014-04-01 12:13 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il: Hi Markus, Thanks, it's is in FSL_DIR /usr/local/fsl. Is MATLAB necessary to run FSL? EIran *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ markus.gschw...@gmail.com] *Sent:* Tuesday, April 01, 2014 12:55 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] preprocessing question Hi, what does it say when you type which fsl which fslmath ? It mud be the same thing as FSL_DIR /usr/local/fsl It is possible that the FSL_DIR specified in the freesurfersetup is not the good one... Best, Markus 2014-04-01 10:25 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il: Hi Markus, Thanks, i did install fsl and when i type fslmaths it gives me the help for that command. Any other suggestions? Eiran -- *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ markus.gschw...@gmail.com] *Sent:* Tuesday, April 01, 2014 11:11 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] preprocessing question Hi! Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/) What happens if you type in your terminal fslmaths ? Best, Markus 2014-04-01 9:59 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il: 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 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo
Re: [Freesurfer] preprocessing question
I'll defer to Doug/Zeke/Nick on this one Bruce On Tue, 1 Apr 2014, Eiran Harel wrote: Thanks Markus. Doug, Bruce, any suggestions? Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.com] Sent: Tuesday, April 01, 2014 4:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question Well, Eiran, That seems all fine. Maybe Bruce or Doug can jump in and help? Sorry! Markus 2014-04-01 15:25 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il: Hi Markus, [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% more $FSL_DIR/etc/fslversion 5.0.6 [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% echo $FSLDIR /usr/local/fsl Thanks! Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.com] Sent: Tuesday, April 01, 2014 2:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question Hi, Although there are matlab utils as part of FSL in $FSL_DIR/etc/matlab that can be used in FSL, I think it is not necessary to have matlab working for FSL to work. There are many more matlab utils in Freesurfer ($FREESURFER_HOME/matlab). The error message tells you that freesurfer doesn't find fslmaths in the fsl directory... Can you post here the exact result of more $FSL_DIR/etc/fslversion and echo $FSLDIR #(without the _ between FSL and DIR!) Best, Markus 2014-04-01 12:13 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il: Hi Markus, Thanks, it's is in FSL_DIR /usr/local/fsl. Is MATLAB necessary to run FSL? EIran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.com] Sent: Tuesday, April 01, 2014 12:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question Hi, what does it say when you type which fsl which fslmath ? It mud be the same thing as FSL_DIR /usr/local/fsl It is possible that the FSL_DIR specified in the freesurfersetup is not the good one… Best, Markus 2014-04-01 10:25 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il: Hi Markus, Thanks, i did install fsl and when i type fslmaths it gives me the help for that command. Any other suggestions? Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.com] Sent: Tuesday, April 01, 2014 11:11 AM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question Hi! Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/) What happens if you type in your terminal fslmaths ? Best, Markus 2014-04-01 9:59 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il: 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 [sign_smallHE_01.jpg] [sign_smallHE_02.jpg] [sign_smallHE_03.jpg] [sign_smallHE_04.jpg] [sign_smallEN_05.jpg] [sign_smallHE_06.jpg] ___ 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. ___ 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
Re: [Freesurfer] preprocessing question
Thanks Markus. Doug, Bruce, any suggestions? Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.com] Sent: Tuesday, April 01, 2014 4:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question Well, Eiran, That seems all fine. Maybe Bruce or Doug can jump in and help? Sorry! Markus 2014-04-01 15:25 GMT+02:00 Eiran Harel eir...@tlvmc.gov.ilmailto:eir...@tlvmc.gov.il: Hi Markus, [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% more $FSL_DIR/etc/fslversion 5.0.6 [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% echo $FSLDIR /usr/local/fsl Thanks! Eiran From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.commailto:markus.gschw...@gmail.com] Sent: Tuesday, April 01, 2014 2:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question Hi, Although there are matlab utils as part of FSL in $FSL_DIR/etc/matlab that can be used in FSL, I think it is not necessary to have matlab working for FSL to work. There are many more matlab utils in Freesurfer ($FREESURFER_HOME/matlab). The error message tells you that freesurfer doesn't find fslmaths in the fsl directory... Can you post here the exact result of more $FSL_DIR/etc/fslversion and echo $FSLDIR #(without the _ between FSL and DIR!) Best, Markus 2014-04-01 12:13 GMT+02:00 Eiran Harel eir...@tlvmc.gov.ilmailto:eir...@tlvmc.gov.il: Hi Markus, Thanks, it's is in FSL_DIR /usr/local/fsl. Is MATLAB necessary to run FSL? EIran From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.commailto:markus.gschw...@gmail.com] Sent: Tuesday, April 01, 2014 12:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question Hi, what does it say when you type which fsl which fslmath ? It mud be the same thing as FSL_DIR /usr/local/fsl It is possible that the FSL_DIR specified in the freesurfersetup is not the good one… Best, Markus 2014-04-01 10:25 GMT+02:00 Eiran Harel eir...@tlvmc.gov.ilmailto:eir...@tlvmc.gov.il: Hi Markus, Thanks, i did install fsl and when i type fslmaths it gives me the help for that command. Any other suggestions? Eiran From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.commailto:markus.gschw...@gmail.com] Sent: Tuesday, April 01, 2014 11:11 AM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question Hi! Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/) What happens if you type in your terminal fslmaths ? Best, Markus 2014-04-01 9:59 GMT+02:00 Eiran Harel eir...@tlvmc.gov.ilmailto:eir...@tlvmc.gov.il: 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/DocLib/SIGN/sign_smallHE_01.jpg]http://www.tasmc.org.il/be-well/Pages/default.aspx [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_02.jpg] https://www.facebook.com/ichilov.medical [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_03.jpg] http://twitter.com/tasmc1 [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_04.jpg] http://www.youtube.com/tasmc1 [http://www.tasmc.org.il/DocLib/SIGN/sign_smallEN_05.jpg] http://www.tasmc.org.il/sites/en/Pages/default.aspx ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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
Re: [Freesurfer] preprocessing question
Hi Doug, No, it does not exist. What should i do? Thanks, Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:16 PM To: 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] preprocessing question
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:16 PM To: 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
Re: [Freesurfer] preprocessing question
Thanks, i can't open the page: Safari can’t open the page “ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac” because Safari can’t load any data from this location. What is the problem? Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] preprocessing question 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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:16 PM To: 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
Re: [Freesurfer] preprocessing question
try now On 04/01/2014 12:53 PM, Eiran Harel wrote: Thanks, i can't open the page: Safari can’t open the page “ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac” because Safari can’t load any data from this location. What is the problem? Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] preprocessing question 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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:16 PM To: 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
Re: [Freesurfer] preprocessing question
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 gr...@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-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [ gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:16 PM To: 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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.
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 gr...@nmr.mgh.harvard.edu mailto:gr...@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-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:16 PM To: 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@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 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr
Re: [Freesurfer] preprocessing question
Do you mean the matrix? You can get a freesurfer matrix with this: cd subject/mri tkregister2 --mov orig/001.mgz --s subject --regheader --reg reg.dat --noedit this will produce reg.dat which will be a text file with a registration matrix. Interpreting the matrix is another story. If you want to map to/from the native space, look at mri_vol2vol (which will use reg.dat). If you want to map to/from the surface, see mri_vol2surf. doug Frederick Klauschen wrote: Could you tell me the transformation vector that is used to convert a e.g.(181x217x181) array to a FS (256^3) array. I would like to backtransform from FS to native space. Thanks, Fred --- Doug Greve [EMAIL PROTECTED] wrote: Which way do you want to go? Convert FS volumes back into the native space or the other way around? To convert native space vols into FS, run something like: tkregister2 --s subjectname --mov mri/orig/001.mgz --regheader --reg reg.dat This will bring up both the conformed and nonconf volumes, and there should be an exact registration. Once you're confidient of that, you can add --noedit in which case it will simply produce reg.dat without bringing up the gui. Then you can run mri_vol2vol --mov anynativevolume --fstarg --o anynativevolume.inconformedspace.mgz The new volume will be in the conformed (orig.mgz) space. doug Goldman, Aaron (NIH/NIMH) [C] wrote: Hi, I have a few datasets I ran in freesurfer that were originally in 181x217x181 format. As usual, these were converted to 256^3 early in the process. Basically, I'd like to run some comparison stats between the freesurfer volumes and the same subjects run in a couple other programs (that are still 181x217x181), and was wondering what the best way would be to reobtain an exact overlay between the two. Thanks, -Aaron- ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] preprocessing question
Could you tell me the transformation vector that is used to convert a e.g.(181x217x181) array to a FS (256^3) array. I would like to backtransform from FS to native space. Thanks, Fred --- Doug Greve [EMAIL PROTECTED] wrote: Which way do you want to go? Convert FS volumes back into the native space or the other way around? To convert native space vols into FS, run something like: tkregister2 --s subjectname --mov mri/orig/001.mgz --regheader --reg reg.dat This will bring up both the conformed and nonconf volumes, and there should be an exact registration. Once you're confidient of that, you can add --noedit in which case it will simply produce reg.dat without bringing up the gui. Then you can run mri_vol2vol --mov anynativevolume --fstarg --o anynativevolume.inconformedspace.mgz The new volume will be in the conformed (orig.mgz) space. doug Goldman, Aaron (NIH/NIMH) [C] wrote: Hi, I have a few datasets I ran in freesurfer that were originally in 181x217x181 format. As usual, these were converted to 256^3 early in the process. Basically, I'd like to run some comparison stats between the freesurfer volumes and the same subjects run in a couple other programs (that are still 181x217x181), and was wondering what the best way would be to reobtain an exact overlay between the two. Thanks, -Aaron- ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] preprocessing question
Hi Frederick, mri_info will give you the various transformations back to native (i.e. scanner) RAS coords. cheers, Bruce On Tue, 29 Aug 2006, Frederick Klauschen wrote: Could you tell me the transformation vector that is used to convert a e.g.(181x217x181) array to a FS (256^3) array. I would like to backtransform from FS to native space. Thanks, Fred --- Doug Greve [EMAIL PROTECTED] wrote: Which way do you want to go? Convert FS volumes back into the native space or the other way around? To convert native space vols into FS, run something like: tkregister2 --s subjectname --mov mri/orig/001.mgz --regheader --reg reg.dat This will bring up both the conformed and nonconf volumes, and there should be an exact registration. Once you're confidient of that, you can add --noedit in which case it will simply produce reg.dat without bringing up the gui. Then you can run mri_vol2vol --mov anynativevolume --fstarg --o anynativevolume.inconformedspace.mgz The new volume will be in the conformed (orig.mgz) space. doug Goldman, Aaron (NIH/NIMH) [C] wrote: Hi, I have a few datasets I ran in freesurfer that were originally in 181x217x181 format. As usual, these were converted to 256^3 early in the process. Basically, I'd like to run some comparison stats between the freesurfer volumes and the same subjects run in a couple other programs (that are still 181x217x181), and was wondering what the best way would be to reobtain an exact overlay between the two. Thanks, -Aaron- ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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
