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
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 eiranh@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.
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschwind@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 <eiranh@tlvmc.gov.ilmailto:eiranh@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
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi, 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 eiranh@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-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ markus.gschwind@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 eiranh@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.
Hi Markus, Thanks, it's is in FSL_DIR /usr/local/fsl. Is MATLAB necessary to run FSL? EIran
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschwind@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 <eiranh@tlvmc.gov.ilmailto:eiranh@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-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 Markus Gschwind [markus.gschwind@gmail.commailto:markus.gschwind@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 <eiranh@tlvmc.gov.ilmailto:eiranh@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
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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 Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi,
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 eiranh@tlvmc.gov.il:
Hi Markus,Thanks, it's is in FSL_DIR /usr/local/fsl. Is MATLAB necessary to run FSL? EIran
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ markus.gschwind@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 eiranh@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-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ markus.gschwind@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 eiranh@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
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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.
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschwind@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 <eiranh@tlvmc.gov.ilmailto:eiranh@tlvmc.gov.il>:
Hi Markus, Thanks, it's is in FSL_DIR /usr/local/fsl. Is MATLAB necessary to run FSL? 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 Markus Gschwind [markus.gschwind@gmail.commailto:markus.gschwind@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 <eiranh@tlvmc.gov.ilmailto:eiranh@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-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 Markus Gschwind [markus.gschwind@gmail.commailto:markus.gschwind@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 <eiranh@tlvmc.gov.ilmailto:eiranh@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 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 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.
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 eiranh@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-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ markus.gschwind@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 eiranh@tlvmc.gov.il:
Hi Markus, Thanks, it's is in FSL_DIR /usr/local/fsl. Is MATLAB necessary to run FSL? EIran
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ markus.gschwind@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 eiranh@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-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ markus.gschwind@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 eiranh@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
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Thanks Markus. Doug, Bruce, any suggestions? Eiran ________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschwind@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 <eiranh@tlvmc.gov.ilmailto:eiranh@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-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 Markus Gschwind [markus.gschwind@gmail.commailto:markus.gschwind@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 <eiranh@tlvmc.gov.ilmailto:eiranh@tlvmc.gov.il>:
Hi Markus, Thanks, it's is in FSL_DIR /usr/local/fsl. Is MATLAB necessary to run FSL? 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 Markus Gschwind [markus.gschwind@gmail.commailto:markus.gschwind@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 <eiranh@tlvmc.gov.ilmailto:eiranh@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-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 Markus Gschwind [markus.gschwind@gmail.commailto:markus.gschwind@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 <eiranh@tlvmc.gov.ilmailto:eiranh@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
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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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschwind@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 eiranh@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschwind@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 eiranh@tlvmc.gov.il: Hi Markus, Thanks, it's is in FSL_DIR /usr/local/fsl. Is MATLAB necessary to run FSL? EIran
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschwind@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 eiranh@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschwind@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 eiranh@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
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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
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Hi Doug, No, it does not exist. What should i do? Thanks, Eiran ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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
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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/
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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 [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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 greve@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/
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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
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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 greve@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 greve@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
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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 greve@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 greve@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
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.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 [
freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [ greve@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 greve@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
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 greve@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
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.edu mailto: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> [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>] > 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 > greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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 <greve@nmr.mgh.harvard.edu mailto: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> [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>] > 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 > greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
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.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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 <greve@nmr.mgh.harvard.edu mailto: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> [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>] > 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 > greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
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.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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 <greve@nmr.mgh.harvard.edu mailto: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> [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>] > 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 > greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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 greve@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
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.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.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [ greve@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-bounces@nmr.mgh.harvard.edu [
freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [ greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
That is weird. You can get a copy from hereftp://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> [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>] > 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 -thresh0.1
>> -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 > greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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/
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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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