Hi Doug, mri_label2vol says it creates an mgz from a label, I need to do the reverse. I'm starting with a mask_MNI.mgz (brought from FSL's MNI space via mri_convert) and I need to be able to use that mask to extract thickness from the individual subject.
Also, mni152reg fails because it expects to write a tmp file into an FSL directory rather than a Freesurfer directory. The FSL standards directory is write protected for obvious reasons. Can I redirect the temporary file? Error message: “mkdir: /usr/local/fsl/data/standard/tmp.fslregister.9446: Permission denied”
Message: 17 Date: Mon, 07 Oct 2013 11:01:23 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces? 116(14) To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5252CCC3.5070601@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Ruth, run mni152reg for each subject to create a registration from the subject to the 152. Then use mri_label2vol to map the mask into each subject's space.
doug
On 10/05/2013 04:08 PM, Ruth Carper wrote:
Doug, I'd like to get them into the individual's space, but I assume I have to get there by way of fsaverage? Final goal is to have a regional thickness measure for each individual subject. Ruth Carper
*From:* "freesurfer-request@nmr.mgh.harvard.edu" freesurfer-request@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Saturday, October 5, 2013 9:00 AM *Subject:* Freesurfer Digest, Vol 116, Issue 14
Message: 1 Date: Fri, 04 Oct 2013 12:21:32 -0400 From: Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces? To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <524EEB0C.8050400@nmr.mgh.harvard.edu mailto:524EEB0C.8050400@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Do you want to transfer them to fsaverage space or to the individual anatomical space? doug
On 10/04/2013 01:42 AM, Ruth Carper wrote:
Hi, I'd like to take some masks that I have in MNI standard space in FSL and map them to Freesurfer surface space. The goal is to extract measures of average cortical thickness (or area or etc) for those regions for each subject. Is there a standard way to do this?
Ruth Carper, PhD Assoc. Project Scientist, UCSD Adjunct Professor, SDSU
Hi Ruth, use this version of mni152reg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
mri_label2vol can go in both directions (and can take any file types, ie, mgz, nii, nii.gz, etc)
doug
On 10/08/2013 01:34 AM, Ruth Carper wrote:
Hi Doug, mri_label2vol says it creates an mgz from a label, I need to do the reverse. I'm starting with a mask_MNI.mgz (brought from FSL's MNI space via mri_convert) and I need to be able to use that mask to extract thickness from the individual subject.
Also, mni152reg fails because it expects to write a tmp file into an FSL directory rather than a Freesurfer directory. The FSL standards directory is write protected for obvious reasons. Can I redirect the temporary file? Error message: “mkdir: /usr/local/fsl/data/standard/tmp.fslregister.9446: Permission denied”
Message: 17 Date: Mon, 07 Oct 2013 11:01:23 -0400 From: Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces? 116(14) To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <5252CCC3.5070601@nmr.mgh.harvard.edu mailto:5252CCC3.5070601@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Ruth, run mni152reg for each subject to create a registration from the subject to the 152. Then use mri_label2vol to map the mask into each subject's space.
doug
On 10/05/2013 04:08 PM, Ruth Carper wrote:
Doug, I'd like to get them into the individual's space, but I assume I have to get there by way of fsaverage? Final goal is to have a regional thickness measure for each individual subject. Ruth Carper
*From:* "freesurfer-request@nmr.mgh.harvard.edu
mailto:freesurfer-request@nmr.mgh.harvard.edu"
<freesurfer-request@nmr.mgh.harvard.edu
mailto:freesurfer-request@nmr.mgh.harvard.edu>
*To:* freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
*Sent:* Saturday, October 5, 2013 9:00 AM *Subject:* Freesurfer Digest, Vol 116, Issue 14
Message: 1 Date: Fri, 04 Oct 2013 12:21:32 -0400 From: 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>> Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces? To: freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
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<mailto:524EEB0C.8050400@nmr.mgh.harvard.edu
mailto:524EEB0C.8050400@nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Do you want to transfer them to fsaverage space or to the individual anatomical space? doug
On 10/04/2013 01:42 AM, Ruth Carper wrote:
Hi, I'd like to take some masks that I have in MNI standard space in FSL and map them to Freesurfer surface space. The goal is to extract measures of average cortical thickness (or area or etc) for those regions for each subject. Is there a standard way to do this?
Ruth Carper, PhD Assoc. Project Scientist, UCSD Adjunct Professor, SDSU
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Douglas Just to check if I correctly understood you, when you said "mri_label2vol can go in both directions" did you mean it can also create a label from a volume or a binary mask? If so, could you please explain how? I read documentation on wiki and help from the command itself and could not see how to accomplish that. I could only find how to create a volume from a label. What I need to do is to get a mask like the binLeftHippoHead.mgz (attached) and create a label. Assuming it is possible, I could also make labels for Hippocampal body and head, merge the 3 labels into an annot file. This way i can use Freeview to load the whole hippocampal surface and discriminate the 3 segments by colors with the annot file. I guess I will get a result like the picture I get after loading lh.pial and lh.aparc.annot. Thank you. Cheers, Marcos. Em Ter, 2013-10-08 às 11:22 -0400, Douglas N Greve escreveu:
Hi Ruth, use this version of mni152reg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
mri_label2vol can go in both directions (and can take any file types, ie, mgz, nii, nii.gz, etc)
doug
On 10/08/2013 01:34 AM, Ruth Carper wrote:
Hi Doug, mri_label2vol says it creates an mgz from a label, I need to do the reverse. I'm starting with a mask_MNI.mgz (brought from FSL's MNI space via mri_convert) and I need to be able to use that mask to extract thickness from the individual subject.
Also, mni152reg fails because it expects to write a tmp file into an FSL directory rather than a Freesurfer directory. The FSL standards directory is write protected for obvious reasons. Can I redirect the temporary file? Error message: “mkdir: /usr/local/fsl/data/standard/tmp.fslregister.9446: Permission denied”
Message: 17 Date: Mon, 07 Oct 2013 11:01:23 -0400 From: Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces? 116(14) To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <5252CCC3.5070601@nmr.mgh.harvard.edu mailto:5252CCC3.5070601@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Ruth, run mni152reg for each subject to create a registration from the subject to the 152. Then use mri_label2vol to map the mask into each subject's space.
doug
On 10/05/2013 04:08 PM, Ruth Carper wrote:
Doug, I'd like to get them into the individual's space, but I assume I have to get there by way of fsaverage? Final goal is to have a regional thickness measure for each individual subject. Ruth Carper
*From:* "freesurfer-request@nmr.mgh.harvard.edu
mailto:freesurfer-request@nmr.mgh.harvard.edu"
<freesurfer-request@nmr.mgh.harvard.edu
mailto:freesurfer-request@nmr.mgh.harvard.edu>
*To:* freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
*Sent:* Saturday, October 5, 2013 9:00 AM *Subject:* Freesurfer Digest, Vol 116, Issue 14
Message: 1 Date: Fri, 04 Oct 2013 12:21:32 -0400 From: 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>> Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces? To: freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID: <524EEB0C.8050400@nmr.mgh.harvard.edu
mailto:524EEB0C.8050400@nmr.mgh.harvard.edu
<mailto:524EEB0C.8050400@nmr.mgh.harvard.edu
mailto:524EEB0C.8050400@nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Do you want to transfer them to fsaverage space or to the individual anatomical space? doug
On 10/04/2013 01:42 AM, Ruth Carper wrote:
Hi, I'd like to take some masks that I have in MNI standard space in FSL and map them to Freesurfer surface space. The goal is to extract measures of average cortical thickness (or area or etc) for those regions for each subject. Is there a standard way to do this?
Ruth Carper, PhD Assoc. Project Scientist, UCSD Adjunct Professor, SDSU
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Marcos Martins da Silva -
Ruth Carper