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

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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

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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

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

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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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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 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

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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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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.

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

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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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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

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

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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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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.

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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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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

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, 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
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 > but does not contain patient information, please contact the
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 > _______________________________________________
 > Freesurfer mailing list
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 <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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