[Freesurfer] Question about talairach.m3z file

[Paul Beach]

Hello Freesurfer community,

I have a question about the file talairach.m3z, which is found in the
mri/transforms directory of all subjects that have undergone recon-all. I
am utilizing this file in an mri_convert script to resample AFNI processed
T1volumes (and time-series data) to MNI space. However, I wanted to confirm
*which* MNI talairach.m3z represents - it's MNI305, correct?


Thanks!
Paul
-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
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[Freesurfer] Fwd: Question about talairach.m3z file

[Paul Beach]

-- Forwarded message --
From: Paul Beach 
Date: Fri, Sep 27, 2013 at 2:39 PM
Subject: Re: [Freesurfer] Question about talairach.m3z file
To: Bruce Fischl 


So would you suggest, then, that it would be better to use the mri_vol2vol
command to transform subject data (anatomical and functional) to MNI space?


On Fri, Sep 27, 2013 at 9:36 AM, Bruce Fischl wrote:

> Hi Paul
>
> not really. It is a nonlinear transform to our own atlas, which is loosely
> in MNI space. Doug can probably give you a more precise answer
>
> cheers
> Bruce
>
> On Fri, 27 Sep 2013, Paul Beach wrote:
>
>  Hello Freesurfer community,
>> I have a question about the file talairach.m3z, which is found in the
>> mri/transforms directory of all subjects that have undergone recon-all. I
>> am
>> utilizing this file in an mri_convert script to resample AFNI processed
>> T1volumes (and time-series data) to MNI space. However, I wanted to
>> confirm
>> which MNI talairach.m3z represents - it's MNI305, correct?
>>
>>
>> Thanks!
>> Paul
>> --
>> Paul Beach
>> DO/PhD candidate - Year VI
>> Michigan State University
>> - College of Osteopathic Medicine
>> - Neuroscience Program   - Bozoki Lab: Neurology/Radiology
>>
>>
>>
>
> 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<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.
>



-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology



-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
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[Freesurfer] MNI152 to 305 conversion

[Paul Beach]

Freesurfer experts,

I'm attempting to utilize an archived e-mail's contents to resample data in
MNI152 to 305.

The script I'm using is as follows:
*mri_vol2vol \*
*--mov
/extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz
\*
*--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz \*
*--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \*
*--inv --o FSL_MNI305_2mm.nii.gz*
*
*
*
*
This series of commands is based on the following suggestion from Doug in a
previously archived e-mail exchange from someone attempting to do something
similar:
*>> To go from mni152 to the MNI305 2mm space, use*
*>>*
*>> mri_vol2vol --mov mni305.2mm.nii.gz \*
*>>  --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \*
*>>  --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \*
*>>  --inv --o output.mni305.2mm.nii.gz*
*>>*
*>> This will resample MNI152_T1_2mm.nii.gz (or anything in that space) to
the*
*>> mni305 2mm space.*


However, this changing the orientation of my data - essentially all images
are being rotated 90degrees so the frontal lobe is pointed straight up.

Are there any suggestions to ameliorate this problem?

Thanks!
-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
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[Freesurfer] running recon-all for FSL-based ROIs

[Paul Beach]

Hello FS experts,

I am interested in utilizing the functional ROIs made by the Greicius lab
out of Stanford (found here<http://findlab.stanford.edu/functional_ROIs.html>).
However, these ROIs were made using FSL and the coordinate system for them
is not responding to simple resampling commands (such as mri_convert or
3dresample). The resulting file from utilizing these commands "works" in
the sense that it puts them in the proper orientation, but the ROIs are
still way out of whack, somehow.

Thus, I would like to try utilizing recon-all to get these ROIs (which
correspond to MNI152-2mm) into the standard space I'm utilizing
(Freesurfer-defined MNI305, based on the subjects' talairach.m3z file).
However, I have no idea how to do this. Could I have some general guidance
on the steps and options for recon-all that would accomplish this?

I have some additional information about the ROIs below.

*This is the 3dinfo output for the ROIs (in this case, anterior-salience)*
Template Space:  TLRC
Dataset Type:Anat Bucket (-abuc)
Byte Order:  LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode:NIFTI
Storage Space:   3,610,516 (3.6 million [mega]) bytes
Geometry String: "MATRIX(2,0,0,-90,0,-2,0,126,0,0,2,-72):91,109,91"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Right-to-Left
  second (y) = Posterior-to-Anterior
  third  (z) = Inferior-to-Superior   [-orient RPI]
R-to-L extent:   -90.000 [R] -to-90.000 [L] -step- 2.000 mm [ 91
voxels]
A-to-P extent:   -90.000 [A] -to-   126.000 [P] -step- 2.000 mm [109
voxels]
I-to-S extent:   -72.000 [I] -to-   108.000 [S] -step- 2.000 mm [ 91
voxels]


Thanks!
-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
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[Freesurfer] mri_surf2surf error - 'could not determine type of...'

[Paul Beach]

Hello FS experts,

I'm attempting to transform the Yeo2011 annotations (lh & rh) from
fsaverage to individual subjects so as to then sample the cortical maps to
subject surfaces using mri_label2vol. However, I'm getting the error in the
subject line when I put in the following commands:

*mri_surf2surf --srcsubject fsaverage \*
*--srcsurfval lh.Yeo2011_17Networks_N1000.annot \*
*--trgsubject HS_001 --trgsurfval lh.Yeo_17Network_native.annot --hemi lh*

I suspected that I have to put a src_type and trg_type in there, but I
wasn't sure what type of types would be appropriate for use in
mri_label2vol. For the latter command I was planning on utilizing something
similar to a previous e-mailer's command (below):
*mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot \*
*--o outfile.nii.gz --hemi lh --subject HS_001 \*
*--temp $SUBJECTS_DIR/HS_001/mri/orig.mgz --identity*

Any suggestions for getting past this error?

Thanks for your help,
Paul
-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
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Re: [Freesurfer] mri_surf2surf error - 'could not determine type of...'

[Paul Beach]

Apologies: the full error message was:
 '*could not determine type of lh.Yeo2011_17Networks_N1000.annot*'

I tried your suggestion of removing the hemispheric designation in front of
'Yeo' and I'm getting the same error - - the same occurs if I remove the
'.annot' at the end.
*mri_surf2surf --srcsubject fsaverage \*
*--srcsurfval Yeo2011_17Networks_N1000.annot \*
*--trgsubject HS_001 --trgsurfval Yeo_17Network_native.annot --hemi lh*
*ERROR: could not determine type of Yeo2011_17Networks_N1000*


Thoughts?

Cheers,
Paul


On Wed, Oct 23, 2013 at 3:49 PM, Douglas N Greve
wrote:

>
> The full error msg is not in the subject line. My guess is that the
> "lh." in front of "Yeo" in the srcsurfval is causing the problem
>
>
> On 10/23/2013 03:17 PM, Paul Beach wrote:
> > Hello FS experts,
> >
> > I'm attempting to transform the Yeo2011 annotations (lh & rh) from
> > fsaverage to individual subjects so as to then sample the cortical
> > maps to subject surfaces using mri_label2vol. However, I'm getting the
> > error in the subject line when I put in the following commands:
> >
> > /mri_surf2surf --srcsubject fsaverage \/
> > /--srcsurfval lh.Yeo2011_17Networks_N1000.annot \/
> > /--trgsubject HS_001 --trgsurfval lh.Yeo_17Network_native.annot --hemi
> lh/
> >
> > I suspected that I have to put a src_type and trg_type in there, but I
> > wasn't sure what type of types would be appropriate for use in
> > mri_label2vol. For the latter command I was planning on utilizing
> > something similar to a previous e-mailer's command (below):
> > /mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot \/
> > /--o outfile.nii.gz --hemi lh --subject HS_001 \/
> > /--temp $SUBJECTS_DIR/HS_001/mri/orig.mgz --identity/
> >
> > Any suggestions for getting past this error?
> >
> > Thanks for your help,
> > Paul
> > --
> > Paul Beach
> > DO/PhD candidate - Year VI
> > Michigan State University
> > - College of Osteopathic Medicine
> > - Neuroscience Program
> >- Bozoki Lab: Neurology/Radiology
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
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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.
>
>


-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
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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
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Re: [Freesurfer] mri_surf2surf error - 'could not determine type of...'

[Paul Beach]

That worked like a charm.

Thanks!


On Wed, Oct 23, 2013 at 5:14 PM, Bruce Fischl wrote:

> try specifying --sval-annot  Yeo2011_17Networks_N1000.annot instead of
> --srcsurfval
>
> cheers
> Bruce
>
> On Wed, 23 Oct 2013, Paul Beach wrote:
>
>  Apologies: the full error message was: 'could not determine type of
>> lh.Yeo2011_17Networks_N1000.**annot'
>> I tried your suggestion of removing the hemispheric designation in front
>> of
>> 'Yeo' and I'm getting the same error - - the same occurs if I remove the
>> '.annot' at the end.
>> mri_surf2surf --srcsubject fsaverage \
>> --srcsurfval Yeo2011_17Networks_N1000.annot \
>> --trgsubject HS_001 --trgsurfval Yeo_17Network_native.annot --hemi lh
>> ERROR: could not determine type of Yeo2011_17Networks_N1000
>>
>>
>> Thoughts?
>>
>> Cheers,
>> Paul
>>
>>
>> On Wed, Oct 23, 2013 at 3:49 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu>
>> wrote:
>>
>>   The full error msg is not in the subject line. My guess is that
>>   the
>>   "lh." in front of "Yeo" in the srcsurfval is causing the problem
>>
>>
>>   On 10/23/2013 03:17 PM, Paul Beach wrote:
>>   > Hello FS experts,
>>   >
>>   > I'm attempting to transform the Yeo2011 annotations (lh & rh)
>>   from
>>   > fsaverage to individual subjects so as to then sample the
>>   cortical
>>   > maps to subject surfaces using mri_label2vol. However, I'm
>>   getting the
>>   > error in the subject line when I put in the following
>>   commands:
>>   >
>> > /mri_surf2surf --srcsubject fsaverage \/
>> > /--srcsurfval lh.Yeo2011_17Networks_N1000.**annot \/
>> > /--trgsubject HS_001 --trgsurfval lh.Yeo_17Network_native.annot
>> --hemi lh/
>> >
>> > I suspected that I have to put a src_type and trg_type in there, but
>> I
>> > wasn't sure what type of types would be appropriate for use in
>> > mri_label2vol. For the latter command I was planning on utilizing
>> > something similar to a previous e-mailer's command (below):
>> > /mri_label2vol --annot lh.Yeo2011_17Networks_N1000.**HS_001.annot \/
>> > /--o outfile.nii.gz --hemi lh --subject HS_001 \/
>> > /--temp $SUBJECTS_DIR/HS_001/mri/orig.**mgz --identity/
>> >
>> > Any suggestions for getting past this error?
>> >
>> > Thanks for your help,
>> > Paul
>> > --
>> > Paul Beach
>> > DO/PhD candidate - Year VI
>> > Michigan State University
>> > - College of Osteopathic Medicine
>> > - Neuroscience Program
>> >- Bozoki Lab: Neurology/Radiology
>> >
>> >
>> > __**_
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> FileDrop: 
>> https://gate.nmr.mgh.harvard.**edu/filedrop2<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/<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<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<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 th

[Freesurfer] converting to fsaverage space

[Paul Beach]

Freesurfer experts,

I am interested in converting functional ROIs defined by the Greicius lab (
http://findlab.stanford.edu/functional_ROIs.html) into individual subject
space. Originally I had converted the fROIs from an FSL-based MNI152 to
Freesurfer-based MNI305 space. To do this I used this command (in this case
for the precuneus network fROI):

*mri_label2vol \*
*--seg Precuneus.nii.gz \*
*--reg $FREESURFER_HOME/average/mni152.register.dat \*
*--invertmtx --o Precuneus_FS.nii.gz \*
*--temp $FREESURFER_HOME/subjects/fsaverage/mri/mni305.cor.mgz*

*The output file's information, provided by 3dinfo, is as follows:*
Template Space:  ORIG
Dataset Type:Anat Bucket (-abuc)
Byte Order:  LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode:NIFTI
Storage Space:   67,108,864 (67 million [mega]) bytes
Geometry String: "MATRIX(1,0,0,-128,0,0,-1,128,0,-1,0,128):256,256,256"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Right-to-Left
  second (y) = Superior-to-Inferior
  third  (z) = Posterior-to-Anterior   [-orient RSP]
R-to-L extent:  -128.000 [R] -to-   127.000 [L] -step- 1.000 mm [256
voxels]
A-to-P extent:  -127.000 [A] -to-   128.000 [P] -step- 1.000 mm [256
voxels]
I-to-S extent:  -127.000 [I] -to-   128.000 [S] -step- 1.000 mm [256
voxels]
Number of values stored at each pixel = 1
  -- At sub-brick #0 '?' datum type is float


I would like to take the output of this command and convert it to an
individual subject's space. However, I'm not really sure how to proceed.

Originally I thought the above command, in using the mni305.cor.mgz file in
fsaverage's mri folder, would put the output file into fsaverage's space. I
could then, I figured, use some other commands I have for moving things in
fsaverage space to individual subject space. Unfortunately, when I try to
load the above output file into tkmedit for fsaverage as an aux volume it's
essentially off screen (i.e. not in the brain). Obviously the output file
is not in fsaverage space, per se.

Any thoughts on how to proceed?

Thanks,
Paul
-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
___
Freesurfer mailing list
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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] Fwd: converting to fsaverage space

[Paul Beach]

Freesurfer experts,

I am interested in converting functional ROIs defined by the Greicius lab (
http://findlab.stanford.edu/functional_ROIs.html) into individual subject
space. Originally I had converted the fROIs from an FSL-based MNI152 to
Freesurfer-based MNI305 space. To do this I used this command (in this case
for the precuneus network fROI):

*mri_label2vol \*
*--seg Precuneus.nii.gz \*
*--reg $FREESURFER_HOME/average/mni152.register.dat \*
*--invertmtx --o Precuneus_FS.nii.gz \*
*--temp $FREESURFER_HOME/subjects/fsaverage/mri/mni305.cor.mgz*

*The output file's information, provided by 3dinfo, is as follows:*
Template Space:  ORIG
Dataset Type:Anat Bucket (-abuc)
Byte Order:  LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode:NIFTI
Storage Space:   67,108,864 (67 million [mega]) bytes
Geometry String: "MATRIX(1,0,0,-128,0,0,-1,128,0,-1,0,128):256,256,256"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Right-to-Left
  second (y) = Superior-to-Inferior
  third  (z) = Posterior-to-Anterior   [-orient RSP]
R-to-L extent:  -128.000 [R] -to-   127.000 [L] -step- 1.000 mm [256
voxels]
A-to-P extent:  -127.000 [A] -to-   128.000 [P] -step- 1.000 mm [256
voxels]
I-to-S extent:  -127.000 [I] -to-   128.000 [S] -step- 1.000 mm [256
voxels]
Number of values stored at each pixel = 1
  -- At sub-brick #0 '?' datum type is float


I would like to take the output of this command and convert it to an
individual subject's space. However, I'm not really sure how to proceed.

Originally I thought the above command, in using the mni305.cor.mgz file in
fsaverage's mri folder, would put the output file into fsaverage's space. I
could then, I figured, use some other commands I have for moving things in
fsaverage space to individual subject space. Unfortunately, when I try to
load the above output file into tkmedit for fsaverage as an aux volume it's
essentially off screen (i.e. not in the brain). Obviously the output file
is not in fsaverage space, per se.

Any thoughts on how to proceed?

Thanks,
Paul
-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
___
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Re: [Freesurfer] Fwd: converting to fsaverage space

[Paul Beach]

Doug,

Thank you for your very helpful suggestion. Indeed, doing so made it so I
could quickly take any parts (or all) of each Greicius network and put them
in individual subject space.

In case this may help anyone else, the final series of commands were (in
this case, for the whole anterior salience network):

*mni152reg --s [subj]*

mri_label2vol
*--seg anterior_Salience.nii.gz \*
--reg $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2mm.dat \
--invertmtx --o anterior_Salience_[subj].nii.gz \
--temp $SUBJECTS_DIR/[subj]/mri/orig.mgz


Cheers,
Paul


On Sun, Dec 1, 2013 at 7:28 PM, Douglas Greve wrote:

>
> Don't go through fsaverage. Instead use mni152reg to create a registration
> matrix from an individual to the 152 (stored in
> $SUBJECTS_DIR/$subject/mri/transforms). Then use the command below with
> this registration matrix instead of mni152.register.dat
>
> doug
>
>
>
> On 11/27/13 2:57 PM, Paul Beach wrote:
>
>  Freesurfer experts,
>
>  I am interested in converting functional ROIs defined by the Greicius
> lab (http://findlab.stanford.edu/functional_ROIs.html) into individual
> subject space. Originally I had converted the fROIs from an FSL-based
> MNI152 to Freesurfer-based MNI305 space. To do this I used this command (in
> this case for the precuneus network fROI):
>
>  *mri_label2vol \*
> *--seg Precuneus.nii.gz \*
> *--reg $FREESURFER_HOME/average/mni152.register.dat \*
> *--invertmtx --o Precuneus_FS.nii.gz \*
>  *--temp $FREESURFER_HOME/subjects/fsaverage/mri/mni305.cor.mgz*
>
>  *The output file's information, provided by 3dinfo, is as follows:*
>  Template Space:  ORIG
>  Dataset Type:Anat Bucket (-abuc)
> Byte Order:  LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
> Storage Mode:NIFTI
> Storage Space:   67,108,864 (67 million [mega]) bytes
> Geometry String: "MATRIX(1,0,0,-128,0,0,-1,128,0,-1,0,128):256,256,256"
> Data Axes Tilt:  Plumb
> Data Axes Orientation:
>   first  (x) = Right-to-Left
>   second (y) = Superior-to-Inferior
>   third  (z) = Posterior-to-Anterior   [-orient RSP]
> R-to-L extent:  -128.000 [R] -to-   127.000 [L] -step- 1.000 mm [256
> voxels]
> A-to-P extent:  -127.000 [A] -to-   128.000 [P] -step- 1.000 mm [256
> voxels]
> I-to-S extent:  -127.000 [I] -to-   128.000 [S] -step- 1.000 mm [256
> voxels]
> Number of values stored at each pixel = 1
>   -- At sub-brick #0 '?' datum type is float
>
>
>  I would like to take the output of this command and convert it to an
> individual subject's space. However, I'm not really sure how to proceed.
>
>  Originally I thought the above command, in using the mni305.cor.mgz file
> in fsaverage's mri folder, would put the output file into fsaverage's
> space. I could then, I figured, use some other commands I have for moving
> things in fsaverage space to individual subject space. Unfortunately, when
> I try to load the above output file into tkmedit for fsaverage as an aux
> volume it's essentially off screen (i.e. not in the brain). Obviously the
> output file is not in fsaverage space, per se.
>
>  Any thoughts on how to proceed?
>
>  Thanks,
> Paul
> --
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
>- Bozoki Lab: Neurology/Radiology
>
>
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-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
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Re: [Freesurfer] Desikan-Killiany parcellations of SI+SII and IPL

[Paul Beach]

I use the Yeo parcellations often for more functionally defined regions.
You should perhaps check out those.

http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011


Cheers


On Thu, Feb 6, 2014 at 7:14 PM, Estephan Moana  wrote:

> Dear Freesurfer experts,
>
> Is it a fair assumption that the Desikan-Killiany parcellations of the
> postcentral gyrus is roughly equivalent to SI+SII, and that the
> supramarginal gyrus ≈ inferior parietal lobule? I used SI, SII and IPL
> ROI masks in some FSL analyses, and would like to use similar ROIs for
> Freesurfer results.
>
> Thank you.
>
> Estephan Moana-Filho, D.D.S., M.S.
> Ph.D. Candidate
> Clinical Fellow, Oral & Maxillofacial Pain Program
> Center for Pain Research and Innovation
> UNC School of Dentistry
> mo...@unc.edu
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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
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-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
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Re: [Freesurfer] hypothalamus?

[Paul Beach]

Ella,

My understanding is the same. I've made my own ROI by hand drawing on the 
average subject and using various commands to map onto individual subjects. If 
you're doing resting analysis then you can check your general whole brain 
correlation results against the literature to see if your ROI performs well. 
It's not perfect, but it can give decent results. 

Cheers,
Paul

Sent from my iPhone

> On Mar 18, 2014, at 7:13 AM, Ella  wrote:
> 
> Hi all,
> 
> I'm looking to create a mask for the hypothalamus on individual subjects. 
> I've had a good look at the literature, and at the moment, am I right in 
> thinking the automatic segmentation in Freesurfer doesn't currently include 
> the hypothalamus?
> 
> thanks in advance
> Ella
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Re: [Freesurfer] Convert processed RS time series to MNI152

[Paul Beach]

Doug,

Thank you for the response. You are correct in that it was originally in
native EPI space. I'll try out your suggestions.

Cheers


On Fri, May 9, 2014 at 1:51 PM, Douglas N Greve
wrote:

>
> What space is the RS data in? If native functional space, I would
> register to the anatomical (bbregister), then use mri_vol2vol with the
> --fstal option
>
> On 05/08/2014 04:31 PM, Paul Beach wrote:
> >> Hi Freesurfers,
> >>
> >> I have several processed resting time series files (processed through
> >> AFNI) and I'd like to convert them to MNI space. I have done this
> >> successfully for T1Volumes and some ROI masks using mri_convert and
> >> tried to use the same code for the resting series. However, I've run
> >> into a few issues - namely that the transformation cuts off part of
> >> the top of the cortex.
> >>
> >> My code:
> >>
> >> /mri_convert -it nii -ot mgz CleanData_RestState.nii.gz
> >> CleanData_RestState.mgz/
> >> /
> >> /
> >> /mri_convert CleanData_RestState.mgz --apply_transform
> >> transforms/talairach.xfm \/
> >> /-oc 0 0 0 CleanData_RestState_talairach.mgz /
> >> /
> >> /
> >> /mri_convert CleanData_RestState_talairach.mgz \
> >> cleanData_RestState_talairach.nii.gz/
> >>
> >>
> >> The final time series file, overlayed on the transformed T1Volume, is
> >> below.
> >>
> >> Inline image 1
> >>
> >> Any suggestions?
> >>
> >>
> >> Thanks!
> >> --
> >> Paul Beach
> >> DO/PhD candidate - Year VI
> >> Michigan State University
> >> - College of Osteopathic Medicine
> >> - Neuroscience Program
> >>  - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
> >
> >
> > ___
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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> is
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-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
 - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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[Freesurfer] mapping extracted MNI152 ROIs to individual subjects

[Paul Beach]

Hello Freesurfer experts,

I am currently trying to take extracted cortical networks from the
Yeo_JNeurophysiol11_MNI152
package<https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011>and
translate them to individual subjects to perform functional
connectivity analyses - based on the individual networks, themselves.
Currently the extracted ROIs are in '.nii.gz' format.

My question is: How do I take the extracted ROIs and map them on to
individual subjects? My thought was that mri_vol2vol could perhaps
accomplish this, but I cannot find a help file for this command that would
guide me in developing the line of code to write.


Thanks!
-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
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[Freesurfer] separate FSAverages and surface-based ROIs

[Paul Beach]

Hello,

I have two issues, currently.

First, I was wondering if it would be possible to create separate FSAverage
brains for different subject groups. I am working with healthy seniors and
various stages of Alzheimer's disease, so doing so would be very helpful
from the perspective of not conflating the differences in neuroanatomy
between the these groups. One idea we had was to create separate HOME
directories for each group, but we wanted to know if there was an easier
way. I can't find anything in the interwebs about this.

Second, I utilize some ROIs that are not specified by FS (such as secondary
somatosensory cortex and anterior vs. posterior insula). My means of
getting around this was to use FSAverage and tksurfer to hand-draw them,
save them as '.label' files, map them to individual subjects, and export
them to AFNI since much of our correlation analysis is done on that
platform. However, I've noticed that when I view these hand-drawn ROIs in
AFNI they only show up at the border of the gray and white matter, rather
than filling the entirety of the gray matter. Note that this problem does
not occur for ROIs in the look up table (like the caudal ACC). Exporting
these to AFNI gives you a nice ROI that fills all the gray matter in the
defined region.

*Code I'm using*:
For the latter problem, what I first use is mri_label2label to map the
fsaverage-based ROI onto individual subjects, for example with the left
anterior insula, before using mri_label2vol:
*mri_label2label --srclabel lh.aIns.label --srcsubject fsaverage --trglabel
lh.aIns.label --trgsubject [subj] --regmethod surface --hemi lh*

*mri_label2vol --label ../label/lh.aIns.label --regheader aparc+aseg.mgz
--o gmroi_volume.nii.gz --temp orig/001.mgz*


Then I copy the new volume file to their AFNI folder, rename it, and run my
correlation analysis on them.

Note, that for those ROIs that are in the look up table (those parcellated
by freesurfer) I simply use mri_label2vol before extracting them using
3dcalc (for example, the caudal anterior cingulate)...
*mri_label2vol --seg aparc+aseg.mgz --regheader aparc+aseg.mgz --o
gmroi_volume.nii.gz --temp orig/001.mgz*

*3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,1002)' -prefix
ROI_FS_lh.caudalACC.nii.gz*



tl:dr
Is it possible to "easily" create multiple FSAverages based on selected
subjects (in my case, subject groups separated by disease state)?

and

Does anyone have any advice on how to get hand-drawn surface-based ROIs
from Freesurfer's tksurfer into AFNI that full cover the entirety of the
gray matter?


Cheers and thanks!
-- 
Paul Beach
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[Freesurfer] extracting hand drawn ROIs to Afni space

[Paul Beach]

Hi there,

Through the help of the Freesurfer Q&A staff I've been able to get ROIs
drawn in tksurfer into an augmented aparc+aseg file of an averaged subject.
I need to be able to get those ROIs, which are not part of the color LUT,
into Afni space.

For ROIs that are already in the LUT, getting them to Afni is no problem, I
simply use a 3dcalc command. However, I have the problem of needing to
export newly parcellated and segmented ROIs that aren't in the Freesurfer
LUT to Afni space.

Is there a way to do this short of creating a new "spot" for them in our
LUT? If not, how does one go about adding ROIs to the LUT and/or creating a
LUT specific to my needs (since the Wiki suggests not fussing with the
original LUT)?


Thanks,
Paul
--
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Re: [Freesurfer] extracting hand drawn ROIs to Afni space

[Paul Beach]

Thank you for forwarding this.

I realize I need to further clarify my issue as well.

With the help of Doug Greve I've taken hand made ROIs in tksurfer,
repackaged them into a new annotation, and repackaged that into a new aseg
file for an average subject. Now (and this is where I'm stuck) I'm trying
to take those newly minted ROIs, place them onto individual subjects'
brains and THEN send them to Afni for each of those subjects (before doing
seed correlation analysis).

Previously I had been using mri_label2label to place the averaged subject
ROI into single subjects' folders and then mri_label2vol to get them ready
to send to Afni. However, this method was not producing ROIs that covered
the extent of a region's gray matter. Thus, Doug's solution of
re-annotating and re-segmenting.

Hopefully that makes things a bit easier.


Thanks again for your help!
Paul


On Mon, Feb 18, 2013 at 3:13 PM, Bruce Fischl wrote:

> Hi Paul
>
> we usually call those labels and have an ascii label file format. Not sure
> how to get that into AFNI, but I'm zure Ziad (ccd) knows.
>
> cheers
> Bruce
>
> On Mon, 18 Feb 2013, Paul Beach wrote:
>
>  Hi there,
>> Through the help of the Freesurfer Q&A staff I've been able to get ROIs
>> drawn in tksurfer into an augmented aparc+aseg file of an averaged
>> subject.
>> I need to be able to get those ROIs, which are not part of the color LUT,
>> into Afni space.
>>
>> For ROIs that are already in the LUT, getting them to Afni is no problem,
>> I
>> simply use a 3dcalc command. However, I have the problem of needing to
>> export newly parcellated and segmented ROIs that aren't in the Freesurfer
>> LUT to Afni space.
>>
>> Is there a way to do this short of creating a new "spot" for them in our
>> LUT? If not, how does one go about adding ROIs to the LUT and/or creating
>> a
>> LUT specific to my needs (since the Wiki suggests not fussing with the
>> original LUT)?
>>
>>
>> Thanks,
>> Paul
>> --
>>
>>
>>
>>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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-- 
Paul Beach
DO/PhD candidate - Year V
Michigan State University
- College of Osteopathic Medicine - OMS V
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
- President: American Physician Scientist Association, MSU COM Chapter
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Re: [Freesurfer] extracting hand drawn ROIs to Afni space

[Paul Beach]

Hi Ziad,

Thank you so much for the suggestions. However, I'm not really sure how to
utilize any of them...So I guess more detailed help would be necessary for
me to follow these suggestions. Sorry.

I've also never actually used SUMA. Previously I was just using a 3dcalc
command to bring aseg ROIs into AFNI space.

I'm not sure if this will make a difference, but I'm dealing with an
averaged subject made with the 'make_average_subject' command (rather than
fsaverage).


Paul


On Tue, Feb 19, 2013 at 10:42 PM, ziad  wrote:

> Hello Paul,
>
> There are a couple of ways I can think of bringing the new ROIs to AFNI
> land from FreeSurfer. I can suggest the following, with the assumption that
> you seek to dump the average time series from single-subject data using an
> ROI defined on the FS average surface.
>
> 1- Get a list from FreeSurfer of the nodes indices that constitute the ROI
> on the FS average surface. That list can take the form of a dataset, that
> we'll call ROI_dset_avg. Use GFTI/NIFTI for surface/volume exchange format
> between FreeSurfer and AFNI.
> 2- Create a standard mesh version of the FS average surface, assuming you
> don't have one already. You can do that much as you would for a regular
> subject using @SUMA_Make_Spec_FS.
> 3- Use SurfToSurf, or MapIcosahedron to map the ROI_dset_avg from the
> original fsaverage surface mesh onto any of the standard-mesh versions of
> fsaverage. We'll call that dataset ROI_dset_avg_std.
> This new dataset can now be used on any of your subject's standardized
> meshes, as long as you use the same icosahedral mesh.
> 4- Create for each subject a volumetric mask of  ROI_dset_avg_std
>  with 3dSurf2Vol
>
> I don't know how well you know how to use the SUMA tools I mentioned
> above, but if you need more detailed help let me know.
>
> cheers,
> Ziad
>
> On Feb 18, 2013, at 4:39 PM, Paul Beach wrote:
>
> Thank you for forwarding this.
>
> I realize I need to further clarify my issue as well.
>
> With the help of Doug Greve I've taken hand made ROIs in tksurfer,
> repackaged them into a new annotation, and repackaged that into a new aseg
> file for an average subject. Now (and this is where I'm stuck) I'm trying
> to take those newly minted ROIs, place them onto individual subjects'
> brains and THEN send them to Afni for each of those subjects (before doing
> seed correlation analysis).
>
> Previously I had been using mri_label2label to place the averaged subject
> ROI into single subjects' folders and then mri_label2vol to get them ready
> to send to Afni. However, this method was not producing ROIs that covered
> the extent of a region's gray matter. Thus, Doug's solution of
> re-annotating and re-segmenting.
>
> Hopefully that makes things a bit easier.
>
>
> Thanks again for your help!
> Paul
>
>
> On Mon, Feb 18, 2013 at 3:13 PM, Bruce Fischl 
> wrote:
>
>> Hi Paul
>>
>> we usually call those labels and have an ascii label file format. Not
>> sure how to get that into AFNI, but I'm zure Ziad (ccd) knows.
>>
>> cheers
>> Bruce
>>
>> On Mon, 18 Feb 2013, Paul Beach wrote:
>>
>>  Hi there,
>>> Through the help of the Freesurfer Q&A staff I've been able to get ROIs
>>> drawn in tksurfer into an augmented aparc+aseg file of an averaged
>>> subject.
>>> I need to be able to get those ROIs, which are not part of the color LUT,
>>> into Afni space.
>>>
>>> For ROIs that are already in the LUT, getting them to Afni is no
>>> problem, I
>>> simply use a 3dcalc command. However, I have the problem of needing to
>>> export newly parcellated and segmented ROIs that aren't in the Freesurfer
>>> LUT to Afni space.
>>>
>>> Is there a way to do this short of creating a new "spot" for them in our
>>> LUT? If not, how does one go about adding ROIs to the LUT and/or
>>> creating a
>>> LUT specific to my needs (since the Wiki suggests not fussing with the
>>> original LUT)?
>>>
>>>
>>> Thanks,
>>> Paul
>>> --
>>>
>>>
>>>
>>>
>>
>> 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<http://www.partners.org/complianceline>.
>>  If the e-mail

Re: [Freesurfer] bbregister to register a .annot file to MNI space

[Paul Beach]

Nathan,

I've run into problems like these before when the fsaverage directory is
read only. This may be behind your "permission denied" error. Perhaps try
to deconstruct the annotation file into your subjects_dir and do the
bbregister command on your label of interest from there - or just copy the
annotation to your subjects_dir...

Cheers


On Mon, May 12, 2014 at 1:34 PM, Nathan Hutcheson  wrote:

> Hello,
>
> I am trying to use bbrestier to take an .annot file of a particular
> structure and register it to MNI space. I want to be able to use one of the
> FreeSurfer parcellations of the ACC (lh.caudalanteriorcingulate.label) and
> do a fMRI BOLD extraction in FSL in MNI space. Below is the command I used
> and the error message I am getting. Please let me know if what I am doing
> makes any sense or if I am way off base.
>
>
> Input
>
>> bbregister --s fsaverage --mov
>> /u/home/n/nhutche/temp/labels/lh.caudalanteriorcingulate.label --t1
>> --init-fsl --reg register.dat
>>
>>
>  Output
>
>> mkdir: cannot create directory `./tmp.bbregister.6489': Permission denied
>>
>> Log file is register.dat.log
>>
>> register.dat.log: Permission denied.
>>
>
>
>
>
>
> Take care,
> Dr. Nathan Hutcheson
> Postdoctoral Researcher
> University of California Los Angeles
> Semel Institute
> 760 Westwood Plaza C8-202
> Los Angeles, CA 90024
> T: 770.841.1694
> nathanhutcheson.com
>  <http://www.linkedin.com/pub/nathan-hutcheson/3a/7a8/a46>
>
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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
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
 - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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[Freesurfer] CTABreadASCII error with mris_label2annot

[Paul Beach]

Freesurfer folks,

I'm trying to compile an annotation using mris_label2annot after
transferring fsaverage5 labels to a single subject. I'm getting a strange
error. Essentially it looks like it can't find most of my transferred
labels, which doesn't make sense as they are definitely in the directory in
which I'm executing the command. The same error happens with both
hemispheres. I am including an 'unknown' entry in the ctab files. I've
tried changing things around with my ctab files and it looks like it just
won't take in anything past the first '-l' flag in the mris_label2annot
command.

*Reading ctab rh.Yeo_7Net_split.ctab*
*Number of ctab entries 2*

*$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $*
*cwd
/extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label*
*cmdline mris_label2annot --s HS_001 --h rh --ctab rh.Yeo_7Net_split.ctab
--annot Yeo_7Net_split_aparc --l
rh.Background+FreeSurfer_Defined_Medial_Wall.label --l
rh.7Networks_RH_Vis.label --l rh.7Networks_RH_SomMot.label --l
rh.7Networks_RH_DorsAttn_Post.label --l rh.7Networks_RH_DorsAttn_FEF.label
--l rh.7Networks_RH_DorsAttn_PrCv.label --l
rh.7Networks_RH_SalVentAttn_TempOccPar.label --l
rh.7Networks_RH_SalVentAttn_PrC.label --l
rh.7Networks_RH_SalVentAttn_FrOper.label --l
rh.7Networks_RH_SalVentAttn_PFCv.label --l
rh.7Networks_RH_SalVentAttn_PFCl.label --l
rh.7Networks_RH_SalVentAttn_Med.label --l rh.7Networks_RH_Limbic_OFC.label
--l rh.7Networks_RH_Limbic_TempPole.label --l
rh.7Networks_RH_Cont_Par.label --l rh.7Networks_RH_Cont_Temp.label --l
rh.7Networks_RH_Cont_PFCv.label --l rh.7Networks_RH_Cont_PFCl.label --l
rh.7Networks_RH_Cont_pCun.label --l rh.7Networks_RH_Cont_Cing.label --l
rh.7Networks_RH_Cont_PFCmp.label --l rh.7Networks_RH_Default_Par.label --l
rh.7Networks_RH_Default_Temp.label --l rh.7Networks_RH_Default_PFCv.label
--l rh.7Networks_RH_Default_PFCm.label --l
rh.7Networks_RH_Default_PCC.label *
*sysname  Linux*
*hostname gauss.rad.msu.edu <http://gauss.rad.msu.edu>*
*machine  x86_64*
*user beachpau*

*subject HS_001*
*hemirh*
*SUBJECTS_DIR /extern/research/PI/training/beachpau/Beach_FreeSurfer_data*
*ColorTable rh.Yeo_7Net_split.ctab*
*AnnotName  Yeo_7Net_split_aparc*
*nlables 26*
*LabelThresh 0 0.00*
*Loading
/extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/surf/rh.orig*
* 1 65793 rh.Background+FreeSurfer_Defined_Medial_Wall*
* 2 -1 NOT_FOUND*
* 3 -1 NOT_FOUND*
* 4 -1 NOT_FOUND*
* 5 -1 NOT_FOUND*
* 6 -1 NOT_FOUND*
* 7 -1 NOT_FOUND*
* 8 -1 NOT_FOUND*
* 9 -1 NOT_FOUND*
*10 -1 NOT_FOUND*
*11 -1 NOT_FOUND*
*12 -1 NOT_FOUND*
*13 -1 NOT_FOUND*
*14 -1 NOT_FOUND*
*15 -1 NOT_FOUND*
*16 -1 NOT_FOUND*
*17 -1 NOT_FOUND*
*18 -1 NOT_FOUND*
*19 -1 NOT_FOUND*
*20 -1 NOT_FOUND*
*21 -1 NOT_FOUND*
*22 -1 NOT_FOUND*
*23 -1 NOT_FOUND*
*24 -1 NOT_FOUND*
*25 -1 NOT_FOUND*
*26 -1 NOT_FOUND*
*Mapping unhit to unknown*
*Found 5 unhit vertices*
*Writing annot to
/extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label/rh.Yeo_7Net_split_aparc.annot*

I have attached my .ctab files in case they would help.
-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
 - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)


lh.Yeo_7Net_split.ctab
Description: Binary data


rh.Yeo_7Net_split.ctab
Description: Binary data
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Re: [Freesurfer] CTABreadASCII error with mris_label2annot

[Paul Beach]

Oy.

Thanks - that worked.


On Wed, May 21, 2014 at 11:21 AM, Douglas N Greve  wrote:

> Your color table appears to have been created in windows (or maybe mac).
> Convert it to a unix text file.
> doug
>
>
> On 05/21/2014 10:40 AM, Paul Beach wrote:
> > Freesurfer folks,
> >
> > I'm trying to compile an annotation using mris_label2annot after
> > transferring fsaverage5 labels to a single subject. I'm getting a
> > strange error. Essentially it looks like it can't find most of my
> > transferred labels, which doesn't make sense as they are definitely in
> > the directory in which I'm executing the command. The same error
> > happens with both hemispheres. I am including an 'unknown' entry in
> > the ctab files. I've tried changing things around with my ctab files
> > and it looks like it just won't take in anything past the first '-l'
> > flag in the mris_label2annot command.
> > /Reading ctab rh.Yeo_7Net_split.ctab/
> > /Number of ctab entries 2/
> > /
> > /
> > /$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $/
> > /cwd
> > /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label/
> > /cmdline mris_label2annot --s HS_001 --h rh --ctab
> > rh.Yeo_7Net_split.ctab --annot Yeo_7Net_split_aparc --l
> > rh.Background+FreeSurfer_Defined_Medial_Wall.label --l
> > rh.7Networks_RH_Vis.label --l rh.7Networks_RH_SomMot.label --l
> > rh.7Networks_RH_DorsAttn_Post.label --l
> > rh.7Networks_RH_DorsAttn_FEF.label --l
> > rh.7Networks_RH_DorsAttn_PrCv.label --l
> > rh.7Networks_RH_SalVentAttn_TempOccPar.label --l
> > rh.7Networks_RH_SalVentAttn_PrC.label --l
> > rh.7Networks_RH_SalVentAttn_FrOper.label --l
> > rh.7Networks_RH_SalVentAttn_PFCv.label --l
> > rh.7Networks_RH_SalVentAttn_PFCl.label --l
> > rh.7Networks_RH_SalVentAttn_Med.label --l
> > rh.7Networks_RH_Limbic_OFC.label --l
> > rh.7Networks_RH_Limbic_TempPole.label --l
> > rh.7Networks_RH_Cont_Par.label --l rh.7Networks_RH_Cont_Temp.label --l
> > rh.7Networks_RH_Cont_PFCv.label --l rh.7Networks_RH_Cont_PFCl.label
> > --l rh.7Networks_RH_Cont_pCun.label --l
> > rh.7Networks_RH_Cont_Cing.label --l rh.7Networks_RH_Cont_PFCmp.label
> > --l rh.7Networks_RH_Default_Par.label --l
> > rh.7Networks_RH_Default_Temp.label --l
> > rh.7Networks_RH_Default_PFCv.label --l
> > rh.7Networks_RH_Default_PFCm.label --l rh.7Networks_RH_Default_PCC.label
> /
> > /sysname  Linux/
> > /hostname gauss.rad.msu.edu <http://gauss.rad.msu.edu>/
> > /machine  x86_64/
> > /user beachpau/
> > /
> > /
> > /subject HS_001/
> > /hemirh/
> > /SUBJECTS_DIR
> /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/
> > /ColorTable rh.Yeo_7Net_split.ctab/
> > /AnnotName  Yeo_7Net_split_aparc/
> > /nlables 26/
> > /LabelThresh 0 0.00/
> > /Loading
> >
> /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/surf/rh.orig/
> > / 1 65793 rh.Background+FreeSurfer_Defined_Medial_Wall/
> > / 2 -1 NOT_FOUND/
> > / 3 -1 NOT_FOUND/
> > / 4 -1 NOT_FOUND/
> > / 5 -1 NOT_FOUND/
> > / 6 -1 NOT_FOUND/
> > / 7 -1 NOT_FOUND/
> > / 8 -1 NOT_FOUND/
> > / 9 -1 NOT_FOUND/
> > /10 -1 NOT_FOUND/
> > /11 -1 NOT_FOUND/
> > /12 -1 NOT_FOUND/
> > /13 -1 NOT_FOUND/
> > /14 -1 NOT_FOUND/
> > /15 -1 NOT_FOUND/
> > /16 -1 NOT_FOUND/
> > /17 -1 NOT_FOUND/
> > /18 -1 NOT_FOUND/
> > /19 -1 NOT_FOUND/
> > /20 -1 NOT_FOUND/
> > /21 -1 NOT_FOUND/
> > /22 -1 NOT_FOUND/
> > /23 -1 NOT_FOUND/
> > /24 -1 NOT_FOUND/
> > /25 -1 NOT_FOUND/
> > /26 -1 NOT_FOUND/
> > /Mapping unhit to unknown/
> > /Found 5 unhit vertices/
> > /Writing annot to
> >
> /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label/rh.Yeo_7Net_split_aparc.annot/
> >
> > I have attached my .ctab files in case they would help.
> > --
> > Paul Beach
> > DO/PhD candidate - Year VI
> > Michigan State University
> > - College of Osteopathic Medicine
> > - Neuroscience Program
> >  - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/f

Re: [Freesurfer] ?reference(s) supporting DLPFC label

[Paul Beach]

Kev,

I can't speak so much to the method you describe in your e-mail, but for my
work I've taken a different approach, owing to certain structures not
currently being parcellated in Freesurfer. Of course, in this case I think
that's because the DLPFC isn't really well defined, anatomically, as much
as it is functionally. Perhaps a better approach would be to frame how you
define your DLPFC region of interest based on your hypothesis.

If you do so you'll find that you can either use prior literature
coordinates or, and this is what I do, you can use functionally-defined
ROIs such as those in the Yeo-parcellations that are now part of Freesurfer
- at least for fsaverage. If you look at the 17Network model you can see a
few different "DLPFC" ROIs that are based on resting-state subnetworks. You
can pick the one you like the most and use various Freesurfer commands to
get them mapped to individual subject space or your standard space of
choice.

I'd be happy to share my scripts with you if you'd like them.

Cheers,
Paul


On Tue, Jun 3, 2014 at 6:02 PM, Fidel Vila  wrote:

> Dear FS community,
>
> I'm looking into DLPFC volume/thickness.
> Following advice posted before on this forum, I'm adding
> G_frontal_middle.label +  S_frontal_inferior.label + S_frontal_middle.label
> from Destrieux 2009 atlas as a surrogate for DLPFC.
>
> My question is whether folks could provide reference(s) from the
> literature backing up this approach?
>
> Thanks for your time and help,
>
> Kev
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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
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> contains patient information, please contact the Partners Compliance
> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
 - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?

[Paul Beach]

Hi Tara,

I do this regularly, though I don't define my Freesurfer ROIs/labels in
QDEC.

*The following will do the process into individual subject space*

*First*:
*mri_label2label *--srclabel path_to_label/label.label --trgsubject {$subj}
--regmethod surface --hemi hemisphere

Do this for as many labels as you have...

*Then*:
Create a color table file (.ctab file) for each hemisphere that contains
your ROIs. Take a look at the FreesurferColorLUT.txt file for help with
that. The first entry should be the Freesurfer defined medial wall, which
you can get from each subject's aparc.annot via mri_annotation2label.

*Then* create an annotation file using your .ctab file and your ROIs - *one
for each hemisphere*

mris_label2annot --s {$subj} --ldir-default --h hemisphere --ctab
hemisphere.ctab_file_name.txt --annot name_for_your_annotation_file \
--l hemi.FS_medial_wall.label \
--l hemi.ROI1.label \
--l hemi.ROI2.label \
--l hemi.ROI3.label \
...

*Then* create a segmentation file from the annotation file

mri_aparc2aseg --s {$subj} --annot
annotion_you_created_without_hemi_designation --o
segmentation_file_name+aseg.mgz

*Then* make a gmroi_vol file from which you can extract your ROIs

mri_label2vol --seg segmentation_file_name+aseg.mgz --regheader
segmentation_file_name+aseg.mgz --o you_gmroi_volume.nii.gz --temp
orig/001.mgz

*Copy the gmroi_vol to your subject's afni directory*

*Use 3dcalc to extract individual ROIs from the gmroi_volume. The number
you put in depends on your .ctab file order. The first ROI would be 1001.
Like the ColorLUT, the first digit being '1' is typically for L. hemi,
while '2' would be for the R. hemi.*

3dcalc -a your_gmroi_volume.nii.gz -expr 'equals(a,)' -prefix
ROI_name.nii.gz


You can then do your AFNI-based analyses with your ROIs.

Hopefully that's all clear. Let me know if I can help in another way.


Cheers,
Paul



On Thu, Jun 5, 2014 at 12:13 PM, Tara Ann Miskovich 
wrote:

> Hi all,
>
> I am wondering if any one has any experience with converting a freesurfer
> surface based ROI created in QDEC into a format I could use on functional
> data in afni.
>
> Thank you,
>
> Tara
>
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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.
>
>


-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
 - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?

[Paul Beach]

Tara,

You have to run the mri_annot2label command on the individual subject's
aparc.annot files (R&L hemi). This will give you the medial wall labels you
can then use to construct your own annotation. You have to include it in
your ctab file, after "unknown."  I think it may be the bankssts.label that
you'll need. Sorry for the confusion about that.

Btw - the ctab (or color table) file is just a text file you can create and
save (either as .ctab or even .txt).

I've attached a .ctab file for reference. Keep in mind that this will look
different from yours as I'm using the Yeo parcellations and they come with
their own medial wall label.




On Mon, Jun 9, 2014 at 11:15 AM, Tara Ann Miskovich 
wrote:

> Thank you Paul that is very helpful, but I could use a little more
> specific help.
>
> A little more context: I ran a group vertexwise analysis with all my
> subjects mapped to the fsaverage and traced my group cluster in QDEC and
> saved the label. Now I would like to somehow get it into afni in the same
> space and use it for some functional analyses.
>
> I mapped the label to each individual subjects space, but the next step I
> am running into issues.
>
> I don't seem to see any medial wall in the aparc annotation. Plus I am not
> familiar with the color table, I was just wondering what that would look
> like.
>
> Any help from anyone would be much appreciated!
>
> Tara
>
> - Original Message -
> From: "Paul Beach" 
> To: "Freesurfer support list" ,
> misko...@uwm.edu
> Sent: Thursday, June 5, 2014 12:26:00 PM
> Subject: Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?
>
>
> Hi Tara,
>
>
> I do this regularly, though I don't define my Freesurfer ROIs/labels in
> QDEC.
>
>
> The following will do the process into individual subject space
>
>
> First :
> mri_label2label --srclabel path_to_label/label.label --trgsubject {$subj}
> --regmethod surface --hemi hemisphere
>
>
> Do this for as many labels as you have...
>
>
> Then :
> Create a color table file (.ctab file) for each hemisphere that contains
> your ROIs. Take a look at the FreesurferColorLUT.txt file for help with
> that. The first entry should be the Freesurfer defined medial wall, which
> you can get from each subject's aparc.annot via mri_annotation2label.
>
>
> Then create an annotation file using your .ctab file and your ROIs - one
> for each hemisphere
>
>
> mris_label2annot --s {$subj} --ldir-default --h hemisphere --ctab
> hemisphere.ctab_file_name.txt --annot name_for_your_annotation_file \
>
> --l hemi.FS_medial_wall.label \
>
> --l hemi.ROI1.label \
> --l hemi.ROI2.label \
>
> --l hemi.ROI3.label \
>
> ...
>
>
> Then create a segmentation file from the annotation file
>
>
> mri_aparc2aseg --s {$subj} --annot
> annotion_you_created_without_hemi_designation --o
> segmentation_file_name+aseg.mgz
>
>
>
> Then make a gmroi_vol file from which you can extract your ROIs
>
>
>
> mri_label2vol --seg segmentation_file_name+aseg.mgz --regheader
> segmentation_file_name+aseg.mgz --o you_gmroi_volume.nii.gz --temp
> orig/001.mgz
>
>
> Copy the gmroi_vol to your subject's afni directory
>
>
> Use 3dcalc to extract individual ROIs from the gmroi_volume. The number
> you put in depends on your .ctab file order. The first ROI would be 1001.
> Like the ColorLUT, the first digit being '1' is typically for L. hemi,
> while '2' would be for the R. hemi.
>
>
> 3dcalc -a your_gmroi_volume.nii.gz -expr 'equals(a,)' -prefix
> ROI_name.nii.gz
>
>
>
>
>
> You can then do your AFNI-based analyses with your ROIs.
>
>
> Hopefully that's all clear. Let me know if I can help in another way.
>
>
>
>
> Cheers,
> Paul
>
>
>
>
>
> On Thu, Jun 5, 2014 at 12:13 PM, Tara Ann Miskovich < misko...@uwm.edu >
> wrote:
>
>
> Hi all,
>
> I am wondering if any one has any experience with converting a freesurfer
> surface based ROI created in QDEC into a format I could use on functional
> data in afni.
>
> Thank you,
>
> Tara
>
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[Freesurfer] Improving translation of Choi striatal ROIs to original domain

[Paul Beach]

Hi Freesurfers,

My processing stream involves moving the parcellated functional networks of
Yeo and Choi to original subject domain to do connectivity analyses. While
my process works very well for the Yeo networks I'm rather unsatisfied by
the results of the Choi translations.

I'm hoping someone has some suggestions for improving things so that the
Choi ROIs map onto individual subjects nearly as well as the general
Freesurfer striatal segmentations.

NB - I work with AD patients, so I'm sure part of the problem is
atrophy-based. However, I'm sure there are ways to improve things...

*My current pipeline involves two steps:*
*mri_vol2vol \*
*--mov Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \*
*--targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader \*
*--o FSL_choi_17Net_MNI152_tight_parcellation.nii.gz --no-save-reg --interp
nearest*

*mri_label2vol \*
*--seg FSL_choi_17Net_MNI152_tight_parcellation.nii.gz \*
*--reg $SUBJECTS_DIR/{$subj}/mri/transforms/reg.mni152.2mm.dat \*
*--invertmtx \*
*--o Choi_17Network_tight_striatum_orig.nii.gz \*
*--temp $SUBJECTS_DIR/{$subj}/mri/orig.mgz*

I suspect one way to improve things would be to do a recon-all based
procedure, but I have no clue what commands within the recon-all domain
that would involve.


Thanks for your suggestions.
-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
 - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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[Freesurfer] Fwd: Improving translation of Choi striatal ROIs to original domain

[Paul Beach]

Hi Freesurfers,

My processing stream involves moving the parcellated functional networks of
Yeo and Choi to original subject domain to do connectivity analyses. While
my process works very well for the Yeo networks I'm rather unsatisfied by
the results of the Choi translations.

I'm hoping someone has some suggestions for improving things so that the
Choi ROIs map onto individual subjects nearly as well as the general
Freesurfer striatal segmentations.

NB - I work with AD patients, so I'm sure part of the problem is
atrophy-based. However, I'm sure there are ways to improve things...

*My current pipeline involves two steps:*
*mri_vol2vol \*
*--mov Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \*
*--targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader \*
*--o FSL_choi_17Net_MNI152_tight_parcellation.nii.gz --no-save-reg --interp
nearest*

*mri_label2vol \*
*--seg FSL_choi_17Net_MNI152_tight_parcellation.nii.gz \*
*--reg $SUBJECTS_DIR/{$subj}/mri/transforms/reg.mni152.2mm.dat \*
*--invertmtx \*
*--o Choi_17Network_tight_striatum_orig.nii.gz \*
*--temp $SUBJECTS_DIR/{$subj}/mri/orig.mgz*

I suspect one way to improve things would be to do a recon-all based
procedure, but I have no clue what commands within the recon-all domain
that would involve.


Thanks for your suggestions.
-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
 - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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Re: [Freesurfer] Fwd: Improving translation of Choi striatal ROIs to original domain

[Paul Beach]

Hi Bruce,

Thanks for the response.

I actually got this pipeline partly from Thomas a few months back. However,
I wasn't sure if anyone had suggestions perhaps for a recon-all based
command for going from the MNI152 1mm template-based fit to individual
subjects. The recon-all/Freesurfer inherent striatal parcellations are so
well fitted to even my severe AD patients, so I was hoping I could somehow
adapt this to the Choi ROIs.


On Wed, Jun 18, 2014 at 8:45 AM, Bruce Fischl 
wrote:

> Hi Paul
>
> Thomas Yeo (ccd) would be the best person to help you, but he may not be
> reading email for a while
>
> cheers
> Bruce
>
>
>
> On Wed, 18 Jun 2014, Paul Beach wrote:
>
>  Hi Freesurfers,
>> My processing stream involves moving the parcellated functional networks
>> of
>> Yeo and Choi to original subject domain to do connectivity analyses. While
>> my process works very well for the Yeo networks I'm rather unsatisfied by
>> the results of the Choi translations.
>>
>> I'm hoping someone has some suggestions for improving things so that the
>> Choi ROIs map onto individual subjects nearly as well as the general
>> Freesurfer striatal segmentations.
>>
>> NB - I work with AD patients, so I'm sure part of the problem is
>> atrophy-based. However, I'm sure there are ways to improve things...
>>
>> My current pipeline involves two steps:
>> mri_vol2vol \
>> --mov Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>> \
>> --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader \
>> --o FSL_choi_17Net_MNI152_tight_parcellation.nii.gz --no-save-reg
>> --interp
>> nearest
>>
>> mri_label2vol \
>> --seg FSL_choi_17Net_MNI152_tight_parcellation.nii.gz \
>> --reg $SUBJECTS_DIR/{$subj}/mri/transforms/reg.mni152.2mm.dat \
>> --invertmtx \
>> --o Choi_17Network_tight_striatum_orig.nii.gz \
>> --temp $SUBJECTS_DIR/{$subj}/mri/orig.mgz
>>
>> I suspect one way to improve things would be to do a recon-all based
>> procedure, but I have no clue what commands within the recon-all domain
>> that
>> would involve.
>>
>>
>> Thanks for your suggestions.
>> --
>> Paul Beach
>> DO/PhD candidate - Year VI
>> Michigan State University
>> - College of Osteopathic Medicine
>> - Neuroscience Program - MSU Cognitive and Geriatric Neurology Team
>> (CoGeNT)
>>
>>
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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
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
 - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Fwd: Improving translation of Choi striatal ROIs to original domain

[Paul Beach]

Thomas,

Thank you so much for this input. I tried out both the striatum and the
general MNI152 template. For the striatum the match is *SO* much better.
The MNI152 template also looks alright - though it's a little fuzzy.

I'm pretty happy with this now and I'll definitely have more confidence in
any striatum-based connectivity differences I see now.

Thanks again.


Paul


On Thu, Jun 19, 2014 at 11:07 AM, Thomas Yeo  wrote:

> Sorry for the slow reply. Here's a (non-ideal) suggestion:
>
> 1) Assuming you are quite happy with the freesurfer striatal parcellation
> in your AD subjects, then I am assuming freesurfer nonlinear registration
> (talairach.m3z) is working quite well. Talairach.m3z warps your subject to
> an internal freesurfer space (kinda like MNI305, but not quite). Let's say
> the freesurfer recon-all output is at /AD_SUBJECT_FS/
>
> 2) Run the MNI152 1mm template (the one from FSL) through recon-all.
> Recon-all will give you a Talairach.m3z that allows you to map the MNI152
> 1mm template to the internal freesurfer space. Let's say the freesurfer
> recon-all output is at /MNI152_FS/
>
> 3) Then do the following:
>
> a) Use mri_vol2vol to upsample the Choi striatal atlas which is 2mm
> resolution to the 1mm MNI152 template:
>
> >> mri_vol2vol --mov Choi_atlas.nii.gz --targ MNI152/mri/norm.mgz
> --regheader --o Choi_atlas1mm.nii.gz --no-save-reg --interp nearest
>
> Notice that I use norm.mgz of the MNI template rather than the original
> MNI template? norm.mgz is the 256 x 256 x 256 conformed version of the MNI
> template that recon-all puts through.
>
> b) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
>
> >> setenv SUBJECTS_DIR 
> >> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ
> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
> Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest
>
> c) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:
>
> >> setenv SUBJECTS_DIR 
> >> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s
> AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z
> talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph
>
>
> This is not optimal because of the double interpolation. You might want to
> use the MNI template instead of the Choi_atlas to test the above, so you
> can check the goodness of the warp. The final warped MNI template should
> hopefully look identical to your AD subject. If that works, then use the
> Choi_atlas. Note that mri_vol2vol does not work properly for talairach.m3z
> below version 5, so you should use version 5x mri_vol2vol.
>
> --Thomas
>
>
>
>
>
>
>
>
>
> On Wed, Jun 18, 2014 at 10:04 PM, Harms, Michael  wrote:
>
>>
>>  Hi,
>> The recon-all based striatal parcellations are based on the anatomy of
>> each particular subject, guided by a probabilistic atlas.  That is
>> inherently likely to be more accurate that just taking a set of
>> ROIs/parcellations defined in some (non-probabilistic) atlas and warping
>> them to each subject via an affine transformation, which is what it sounds
>> like you are doing with the "Choi ROIs".
>>
>>  cheers,
>> -MH
>>
>>   --
>> Michael Harms, Ph.D.
>>  ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>
>>   From: Paul Beach 
>> Reply-To: Freesurfer support list 
>> Date: Wednesday, June 18, 2014 8:52 AM
>> To: Freesurfer support list 
>> Cc: Thomas Yeo , "Yeo, Boon Thye Thomas -- Boon
>> Thye Thomas Yeo" 
>> Subject: Re: [Freesurfer] Fwd: Improving translation of Choi striatal
>> ROIs to original domain
>>
>>   Hi Bruce,
>>
>>  Thanks for the response.
>>
>>  I actually got this pipeline partly from Thomas a few months back.
>> However, I wasn't sure if anyone had suggestions perhaps for a recon-all
>> based command for going from the MNI152 1mm template-based fit to
>> individual subjects. The recon-all/Freesurfer inherent striatal
>> parcellations are so well fitted to even my severe AD patients, so I was
>> hoping I could somehow adapt this to the Choi ROIs.
>>
>>
>> On Wed, Jun 18, 2014 at 8:45 AM, Bruce Fischl > > wrote:
>>
>>> Hi Paul
>>>
>>> Thomas Yeo (ccd) would be the best person t

Re: [Freesurfer] insula on medial surface

[Paul Beach]

I asked a neuroanatomist and insula expert on my campus about this a while
back and this was his response:

"This is the region of the "limen insulae" that you will remember Dr.
Heimer referring to often in the brain dissection course. The insula is
defined as cortex which is covered by a lid of other cortical lobes,
frontal, parietal and temporal. They all fold over except at the inferior
frontal end where a little bit of the surface of otherwise insular cortex
is not covered, and this little corner peeks out. This is the limeninsula which
neighbors the olfactory cortex on the inferior surface of the frontal lobe
and the medial surface of the temporal lobe, and is olfactory cortex
itself. Since it is not covered over, it technically might not be
considered really "insular" but it is obviously in continuity with, and not
separated by any kind of sulcus or other landmark, from the rest of the
insular covered cortex. So we are left with no secure boundary line between
insular cortex and inferior frontal and medial temporal cortex in this
corner. It looks like Freesurfer has decided to call it all insular, and
with good functional reasons."


Cheers,



On Thu, Aug 7, 2014 at 3:32 PM, Bruce Fischl 
wrote:

> Hi Mike
>
> I'm not sure - I think the insula was an additional label that Ron
> Killiany added. I'll cc Ron to see if he has any insight. It certainly
> looks too medial to me.
>
> I would also check on the white surface just to make sure that it's not a
> quirk of the inflation. If the aseg looks right we could certainly put
> together some simple auto-editing to correct this kind of thing
>
> cheers
> Bruce
>
>
>
> On Thu, 7 Aug 2014, Harms, Michael wrote:
>
>
>> Hi,
>> An astute RA, while reviewing the aparc+aseg.mgz of brains processed with
>> FS
>> 5.3, noticed a fair number of instances, where the insula label "wraps
>> around" pretty medially, where she was expecting to see orbitofrontal as
>> the
>> label.  See attached jpg's for two examples shown on the inflated surface.
>>  Since this is fairly common, I'm assuming that this isn't anything to be
>> concerned about, but just wanted to confirm.
>>
>> Has this always been the behavior of the insula label, and we just didn't
>> notice it previously?
>>
>> thanks,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>
>>
>>
>>
>> 
>> 
>>
>>
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the
>> contents
>> of this information is strictly prohibited. If you have received this
>> email
>> in error, please immediately notify the sender via telephone or return
>> mail.
>>
>>
>>
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-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
 - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

[Paul Beach]

The general fsaverage (as well as it's other iterations, fsaverages 3-6)
should be located in your $FREESURFER_HOME/subjects directory. You could
symbolically link it over to your $SUBJECTS_DIR.

On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud  wrote:

> Dear All,
>
> I ran the following script:
>
> #!/bin/bash
> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
> recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm
> -subject case022_tp2 -all
>
> and got the error below at the end. Could anybody please let me know how
> to fix it.
>
> Thank you,
> Mahmoud
>
>
> Reporting on  70 segmentations
> mri_segstats done
> /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label
> #
> #@# BA Labels lh Tue Sep 16 19:26:47 PDT 2014
> INFO: *fsaverage subject does not exist in SUBJECTS_DIR*
> INFO: Creating symlink to fsaverage subject...
>
>  cd /mnt/hgfs/DBSI/volumetric/MGZ; ln -s
> /usr/local/freesurfer/subjects/fsaverage; cd -
>
> ln: *failed to create symbolic link './fsaverage': Operation not
> supported*
>
>  mri_label2label --srcsubject fsaverage --srclabel
> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label --trgsubject
> case022_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
>
> No such file or directory
> mri_label2label: could not open label file
> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
>
> srclabel = /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
> srcsubject = fsaverage
> trgsubject = case022_tp2
> trglabel = ./lh.BA1.label
> regmethod = surface
>
> srchemi = lh
> trghemi = lh
> trgsurface = white
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> usehash = 1
> Use ProjAbs  = 0, 0
> Use ProjFrac = 0, 0
> DoPaint 0
>
> SUBJECTS_DIR/mnt/hgfs/DBSI/volumetric/MGZ
> FREESURFER_HOME /usr/local/freesurfer
> Loading source label.
> Invalid argument
> ERROR reading /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
> Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s case022_tp2 exited with ERRORS at Tue Sep 16 19:26:47 PDT 2014
>
> For more details, see the log file
> /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
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>
>
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-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
 - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

[Paul Beach]

Try something like:

cd $SUBJECTS_DIR
ln -s $FREESURFER_HOME/subjects/fsaverage .

Confirm the linked directory is now in your $SUBJECTS_DIR, then try running
your script.

On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud  wrote:

> Paul,
>
> The fsaverages are in $FREESURFER_HOME/subjects. So does it mean that the
> program couldn't make a link between my actual image places and 
> $FREESURFER_HOME/subjects/fsaverage
> ?
> what can I do to fix it ?
>
> Thank you,
> Mahmoud
>
> On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach  wrote:
>
>> The general fsaverage (as well as it's other iterations, fsaverages 3-6)
>> should be located in your $FREESURFER_HOME/subjects directory. You could
>> symbolically link it over to your $SUBJECTS_DIR.
>>
>> On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud  wrote:
>>
>>> Dear All,
>>>
>>> I ran the following script:
>>>
>>> #!/bin/bash
>>> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
>>> recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm
>>> -subject case022_tp2 -all
>>>
>>> and got the error below at the end. Could anybody please let me know how
>>> to fix it.
>>>
>>> Thank you,
>>> Mahmoud
>>>
>>>
>>> Reporting on  70 segmentations
>>> mri_segstats done
>>> /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label
>>> #
>>> #@# BA Labels lh Tue Sep 16 19:26:47 PDT 2014
>>> INFO: *fsaverage subject does not exist in SUBJECTS_DIR*
>>> INFO: Creating symlink to fsaverage subject...
>>>
>>>  cd /mnt/hgfs/DBSI/volumetric/MGZ; ln -s
>>> /usr/local/freesurfer/subjects/fsaverage; cd -
>>>
>>> ln: *failed to create symbolic link './fsaverage': Operation not
>>> supported*
>>>
>>>  mri_label2label --srcsubject fsaverage --srclabel
>>> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label --trgsubject
>>> case022_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
>>>
>>> No such file or directory
>>> mri_label2label: could not open label file
>>> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
>>>
>>> srclabel = /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
>>> srcsubject = fsaverage
>>> trgsubject = case022_tp2
>>> trglabel = ./lh.BA1.label
>>> regmethod = surface
>>>
>>> srchemi = lh
>>> trghemi = lh
>>> trgsurface = white
>>> srcsurfreg = sphere.reg
>>> trgsurfreg = sphere.reg
>>> usehash = 1
>>> Use ProjAbs  = 0, 0
>>> Use ProjFrac = 0, 0
>>> DoPaint 0
>>>
>>> SUBJECTS_DIR/mnt/hgfs/DBSI/volumetric/MGZ
>>> FREESURFER_HOME /usr/local/freesurfer
>>> Loading source label.
>>> Invalid argument
>>> ERROR reading /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
>>> Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC
>>> 2014 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s case022_tp2 exited with ERRORS at Tue Sep 16 19:26:47 PDT
>>> 2014
>>>
>>> For more details, see the log file
>>> /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/scripts/recon-all.log
>>> To report a problem, see
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>
>>>
>>> ___
>>> 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.
>>>
>>>
>>
>>
>> --
>> Paul Beach
>> DO/PhD candidate - Year VI
>> Michigan State University
>> - College of Osteopathic Medicine
>> - Neuroscience Program
>>  - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.e

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

[Paul Beach]

you have to tell the symbolic link where to put the directory

copy this exactly into your terminal, including the period at the end

SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
cd $SUBJECTS_DIR
ln -s $FREESURFER_HOME/subjects/fsaverage .



On Wed, Sep 17, 2014 at 9:46 AM, Mahmoud  wrote:

> Paul,
>
> I tried this:
> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
> cd $SUBJECTS_DIR
> ln -s $FREESURFER_HOME/subjects/fsaverage
>
> and got this:
> ln: failed to create symbolic link ‘./fsaverage’: Operation not supported
>
> any idea ?
>
> Mahmoud
>
> On Wed, Sep 17, 2014 at 6:27 AM, Paul Beach  wrote:
>
>> Try something like:
>>
>> cd $SUBJECTS_DIR
>> ln -s $FREESURFER_HOME/subjects/fsaverage .
>>
>> Confirm the linked directory is now in your $SUBJECTS_DIR, then try
>> running your script.
>>
>> On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud  wrote:
>>
>>> Paul,
>>>
>>> The fsaverages are in $FREESURFER_HOME/subjects. So does it mean that
>>> the program couldn't make a link between my actual image places and 
>>> $FREESURFER_HOME/subjects/fsaverage
>>> ?
>>> what can I do to fix it ?
>>>
>>> Thank you,
>>> Mahmoud
>>>
>>> On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach  wrote:
>>>
>>>> The general fsaverage (as well as it's other iterations, fsaverages
>>>> 3-6) should be located in your $FREESURFER_HOME/subjects directory. You
>>>> could symbolically link it over to your $SUBJECTS_DIR.
>>>>
>>>> On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud  wrote:
>>>>
>>>>> Dear All,
>>>>>
>>>>> I ran the following script:
>>>>>
>>>>> #!/bin/bash
>>>>> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
>>>>> recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm
>>>>> -subject case022_tp2 -all
>>>>>
>>>>> and got the error below at the end. Could anybody please let me know
>>>>> how to fix it.
>>>>>
>>>>> Thank you,
>>>>> Mahmoud
>>>>>
>>>>>
>>>>> Reporting on  70 segmentations
>>>>> mri_segstats done
>>>>> /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label
>>>>> #
>>>>> #@# BA Labels lh Tue Sep 16 19:26:47 PDT 2014
>>>>> INFO: *fsaverage subject does not exist in SUBJECTS_DIR*
>>>>> INFO: Creating symlink to fsaverage subject...
>>>>>
>>>>>  cd /mnt/hgfs/DBSI/volumetric/MGZ; ln -s
>>>>> /usr/local/freesurfer/subjects/fsaverage; cd -
>>>>>
>>>>> ln: *failed to create symbolic link './fsaverage': Operation not
>>>>> supported*
>>>>>
>>>>>  mri_label2label --srcsubject fsaverage --srclabel
>>>>> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label --trgsubject
>>>>> case022_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
>>>>>
>>>>> No such file or directory
>>>>> mri_label2label: could not open label file
>>>>> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
>>>>>
>>>>> srclabel = /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
>>>>> srcsubject = fsaverage
>>>>> trgsubject = case022_tp2
>>>>> trglabel = ./lh.BA1.label
>>>>> regmethod = surface
>>>>>
>>>>> srchemi = lh
>>>>> trghemi = lh
>>>>> trgsurface = white
>>>>> srcsurfreg = sphere.reg
>>>>> trgsurfreg = sphere.reg
>>>>> usehash = 1
>>>>> Use ProjAbs  = 0, 0
>>>>> Use ProjFrac = 0, 0
>>>>> DoPaint 0
>>>>>
>>>>> SUBJECTS_DIR/mnt/hgfs/DBSI/volumetric/MGZ
>>>>> FREESURFER_HOME /usr/local/freesurfer
>>>>> Loading source label.
>>>>> Invalid argument
>>>>> ERROR reading
>>>>> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
>>>>> Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC
>>>>> 2014 x86_64 x86_64 x86_64 GNU/Linux
>>>>>
>>>>> recon-all -s case022_tp2 exited with ERRORS at Tue Sep 16 19:26:47 PDT
>>>>> 2014
>>>>>
>>>>> For more details, see the log file
>>>>&

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

[Paul Beach]

Hmm. Well I'm stumped. Sorry.  :-/

Any Freesurfer gurus have some ideas here?

On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud  wrote:

> Paul
>
> it shows again:
> ln: failed to create symbolic link ‘./fsaverage’: Operation not supported
>
> !!!
>
> On Wed, Sep 17, 2014 at 6:50 AM, Paul Beach  wrote:
>
>> you have to tell the symbolic link where to put the directory
>>
>> copy this exactly into your terminal, including the period at the end
>>
>> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
>> cd $SUBJECTS_DIR
>> ln -s $FREESURFER_HOME/subjects/fsaverage .
>>
>>
>>
>> On Wed, Sep 17, 2014 at 9:46 AM, Mahmoud  wrote:
>>
>>> Paul,
>>>
>>> I tried this:
>>> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
>>> cd $SUBJECTS_DIR
>>> ln -s $FREESURFER_HOME/subjects/fsaverage
>>>
>>> and got this:
>>> ln: failed to create symbolic link ‘./fsaverage’: Operation not supported
>>>
>>> any idea ?
>>>
>>> Mahmoud
>>>
>>> On Wed, Sep 17, 2014 at 6:27 AM, Paul Beach  wrote:
>>>
>>>> Try something like:
>>>>
>>>> cd $SUBJECTS_DIR
>>>> ln -s $FREESURFER_HOME/subjects/fsaverage .
>>>>
>>>> Confirm the linked directory is now in your $SUBJECTS_DIR, then try
>>>> running your script.
>>>>
>>>> On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud  wrote:
>>>>
>>>>> Paul,
>>>>>
>>>>> The fsaverages are in $FREESURFER_HOME/subjects. So does it mean that
>>>>> the program couldn't make a link between my actual image places and 
>>>>> $FREESURFER_HOME/subjects/fsaverage
>>>>> ?
>>>>> what can I do to fix it ?
>>>>>
>>>>> Thank you,
>>>>> Mahmoud
>>>>>
>>>>> On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach 
>>>>> wrote:
>>>>>
>>>>>> The general fsaverage (as well as it's other iterations, fsaverages
>>>>>> 3-6) should be located in your $FREESURFER_HOME/subjects directory. You
>>>>>> could symbolically link it over to your $SUBJECTS_DIR.
>>>>>>
>>>>>> On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud  wrote:
>>>>>>
>>>>>>> Dear All,
>>>>>>>
>>>>>>> I ran the following script:
>>>>>>>
>>>>>>> #!/bin/bash
>>>>>>> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
>>>>>>> recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm
>>>>>>> -subject case022_tp2 -all
>>>>>>>
>>>>>>> and got the error below at the end. Could anybody please let me know
>>>>>>> how to fix it.
>>>>>>>
>>>>>>> Thank you,
>>>>>>> Mahmoud
>>>>>>>
>>>>>>>
>>>>>>> Reporting on  70 segmentations
>>>>>>> mri_segstats done
>>>>>>> /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label
>>>>>>> #
>>>>>>> #@# BA Labels lh Tue Sep 16 19:26:47 PDT 2014
>>>>>>> INFO: *fsaverage subject does not exist in SUBJECTS_DIR*
>>>>>>> INFO: Creating symlink to fsaverage subject...
>>>>>>>
>>>>>>>  cd /mnt/hgfs/DBSI/volumetric/MGZ; ln -s
>>>>>>> /usr/local/freesurfer/subjects/fsaverage; cd -
>>>>>>>
>>>>>>> ln: *failed to create symbolic link './fsaverage': Operation not
>>>>>>> supported*
>>>>>>>
>>>>>>>  mri_label2label --srcsubject fsaverage --srclabel
>>>>>>> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label --trgsubject
>>>>>>> case022_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
>>>>>>>
>>>>>>> No such file or directory
>>>>>>> mri_label2label: could not open label file
>>>>>>> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
>>>>>>>
>>>>>>> srclabel = /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
>>>>>>> srcsubject = fsaverage
>>>>>>> trgsubject = case022_tp2
>>>>>>> 

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

[Paul Beach]

Yeah, I was starting to wonder if he was having permissions issues as well.

On Wed, Sep 17, 2014 at 10:16 AM, Mahmoud  wrote:

> Paul,
>
> I am using bash instead of tcsh. Does it make any difference ?
>
> Mahmoud
>
> On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach  wrote:
>
>> Hmm. Well I'm stumped. Sorry.  :-/
>>
>> Any Freesurfer gurus have some ideas here?
>>
>> On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud  wrote:
>>
>>> Paul
>>>
>>> it shows again:
>>> ln: failed to create symbolic link ‘./fsaverage’: Operation not supported
>>>
>>> !!!
>>>
>>> On Wed, Sep 17, 2014 at 6:50 AM, Paul Beach  wrote:
>>>
>>>> you have to tell the symbolic link where to put the directory
>>>>
>>>> copy this exactly into your terminal, including the period at the end
>>>>
>>>> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
>>>> cd $SUBJECTS_DIR
>>>> ln -s $FREESURFER_HOME/subjects/fsaverage .
>>>>
>>>>
>>>>
>>>> On Wed, Sep 17, 2014 at 9:46 AM, Mahmoud  wrote:
>>>>
>>>>> Paul,
>>>>>
>>>>> I tried this:
>>>>> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
>>>>> cd $SUBJECTS_DIR
>>>>> ln -s $FREESURFER_HOME/subjects/fsaverage
>>>>>
>>>>> and got this:
>>>>> ln: failed to create symbolic link ‘./fsaverage’: Operation not
>>>>> supported
>>>>>
>>>>> any idea ?
>>>>>
>>>>> Mahmoud
>>>>>
>>>>> On Wed, Sep 17, 2014 at 6:27 AM, Paul Beach 
>>>>> wrote:
>>>>>
>>>>>> Try something like:
>>>>>>
>>>>>> cd $SUBJECTS_DIR
>>>>>> ln -s $FREESURFER_HOME/subjects/fsaverage .
>>>>>>
>>>>>> Confirm the linked directory is now in your $SUBJECTS_DIR, then try
>>>>>> running your script.
>>>>>>
>>>>>> On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud  wrote:
>>>>>>
>>>>>>> Paul,
>>>>>>>
>>>>>>> The fsaverages are in $FREESURFER_HOME/subjects. So does it mean
>>>>>>> that the program couldn't make a link between my actual image places 
>>>>>>> and $FREESURFER_HOME/subjects/fsaverage
>>>>>>> ?
>>>>>>> what can I do to fix it ?
>>>>>>>
>>>>>>> Thank you,
>>>>>>> Mahmoud
>>>>>>>
>>>>>>> On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach 
>>>>>>> wrote:
>>>>>>>
>>>>>>>> The general fsaverage (as well as it's other iterations, fsaverages
>>>>>>>> 3-6) should be located in your $FREESURFER_HOME/subjects directory. You
>>>>>>>> could symbolically link it over to your $SUBJECTS_DIR.
>>>>>>>>
>>>>>>>> On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud 
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Dear All,
>>>>>>>>>
>>>>>>>>> I ran the following script:
>>>>>>>>>
>>>>>>>>> #!/bin/bash
>>>>>>>>> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
>>>>>>>>> recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm
>>>>>>>>> -subject case022_tp2 -all
>>>>>>>>>
>>>>>>>>> and got the error below at the end. Could anybody please let me
>>>>>>>>> know how to fix it.
>>>>>>>>>
>>>>>>>>> Thank you,
>>>>>>>>> Mahmoud
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Reporting on  70 segmentations
>>>>>>>>> mri_segstats done
>>>>>>>>> /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label
>>>>>>>>> #
>>>>>>>>> #@# BA Labels lh Tue Sep 16 19:26:47 PDT 2014
>>>>>>>>> INFO: *fsaverage subject does not exist in SUBJECTS_DIR*
>>>>>>>>> INFO: Creating symlink to fsaverage subject...
>>>>