Re: [Freesurfer] (no subject)

[Douglas N. Greve]

   External Email - Use Caution

SVM is a segmentation/classification algorithm and does not give the 
inference that the GLM gives. Not sure what other models you are talking 
about


On 8/21/2023 9:28 AM, 林 耀云 wrote:


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Hi Freesurfer Team,

I have a question can’t understand. Why  just uses general linear 
model to analysis in Freesurfer? There are a lot of models such as 
nonlinear model, SVM and others. Please help me answer. Thank you so 
much. Additionally, as attached picture, Do we need to transform all 
the data to the coronal plane? Can’t be a sagittal and axial plane?


Thanks so much!

Best,

Yaoyun


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Re: [Freesurfer] (no subject)

[Nolan, Jackson]

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Hello,

'timepoints' refers to the individual scan sessions that make up a longitudinal 
dataset for a subject.

i.e. If a subject was scanned 3 times, say in 2010, 2015, and 2020, this 
subject would have 3 timepoints. One from each year they were scanned.

Best,
Jackson

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Atwater, Emanuel R 

Sent: Thursday, July 27, 2023 6:15 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] (no subject)


External Email - Use Caution

Hello FreeSurfer Team,



I recently messaged about running a longitudinal scan on a couple of images.



The response told me to utilize “timepoints”:

For base processing, specify each timepoint with -tp <> (not the nii file).

recon-all -base  -tp  -tp  ... -all



I’ve attempted to review the youtube videos and instructions made available 
online but am unsure what “timepoints” are. Can I have some clarification on 
what exactly a timepoint is, please.



FS version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b

Recon-all.log: see attached



V/r,

Emanuel Atwater


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Re: [Freesurfer] (no subject)

[Douglas N. Greve]

Not sure. I think those distortions are the surface folding back in on 
itself, so you may need more cuts.


On 5/25/2022 9:26 AM, Alberto Pisoni wrote:


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Hi all, I am trying to flatten a whole hemisphere, and i created the 
cut patch following the tutorials.


see the result here.

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Then I run the command

mris_flatten  

from the surf dir and it works, but when I visualize the patch it is 
distorted, like if I did not cut the inflated surface.


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What am I missing?

The Freesurfer version is 7.2.0 (although I also tried with 6.0) and 
the system is a OS 11.6.1 BigSur Macbook Pro with M1 chip.


Thanks

Alberto

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Re: [Freesurfer] Average subject and head size

[Sébastien Daligault]

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Thank you for the answer.
So the averaged MRI has the size of the mni305.
Is there a way to give it its true size?
This can be problematic for children's MRIs.

> Le 2 mai 2022 à 21:33, Douglas N. Greve  a écrit :
> 
> It will remain in talairach space ( actually mni305)
> 
> 
> On 5/2/2022 1:08 PM, Sébastien Daligault wrote:
>> External Email - Use Caution
>> 
>> Hi support,
>> I have a naive question about the make_average_subject function.
>> I want to average MRIs to create a template.
>> This process uses the talairach transformation to average in a common space. 
>> Once averaged, is the MRI still in this space or is there an inverse 
>> transformation to return to a real size? (which would be the average size of 
>> talairach boxes).
>> Thank you in advance for your answer.
>> Sebastien
>> 
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Re: [Freesurfer] Average subject and head size

[Douglas N. Greve]

It will remain in talairach space ( actually mni305)


On 5/2/2022 1:08 PM, Sébastien Daligault wrote:
>  External Email - Use Caution
>
> Hi support,
> I have a naive question about the make_average_subject function.
> I want to average MRIs to create a template.
> This process uses the talairach transformation to average in a common space. 
> Once averaged, is the MRI still in this space or is there an inverse 
> transformation to return to a real size? (which would be the average size of 
> talairach boxes).
> Thank you in advance for your answer.
> Sebastien
>
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Re: [Freesurfer] (no subject)

[Fischl, Bruce]

Just give freeview the path to whatever volume or surface you want to visualize

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jabeur Mouna
Sent: Wednesday, April 27, 2022 5:45 AM
To: Freesurfer support list 
Subject: [Freesurfer] (no subject)


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Hello,

How can i import an image.nii from a folder different from  
/usr/local/freesurfer/7.2.0/subjects to visualise it with freeview ?

Please!
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Re: [Freesurfer] (no subject)

[Stephanie K]

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Hello,

Can you please clarify the following:

Do we use subcortical QC rating for all subcortical measures such as
accumbens as well measures such as total white matter volume. We do not use
it for estimated total intracranial volume as this is accurately measured?

Do we use cortical QC rating for all regional cortical measures but not the
global measures (e.g. mean thickness/total surface area) as these are
accurately parcellated?

Sorry for my very basic questions. I am using already processed data and
only using the statistics for brain MRI data

Thanks,
Stephanie
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Re: [Freesurfer] (no subject)

[Douglas N. Greve]

No, it should not

On 6/22/2021 4:12 PM, miracle ozzoude wrote:


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Hello All,

I was wondering if the  Right/Left-Cerebral-White-Matter in the 
aparc+aseg.mgz contains WM hypointensities.


mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats 
--ctab FreeSurferColorLUT.txt


Best,
Paul

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Re: [Freesurfer] (no subject)

[Francisca Ferreira]

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Hi Doug,

I ran
mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C
groupdiff.mtx \--glmdir aseg.glmdir

this created a folder aseg.glmdir which contains another folder groupdiff,
where sig.ghm is,

I then tried to visualise results using

freeview -f
/usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5
-viewport 3d

Many thanks in advance!

Francisca


On Tue, Jun 1, 2021 at 1:40 AM Douglas N. Greve 
wrote:

> How did you create the sig.mgh that you are trying to overlay?
>
> On 5/28/2021 11:16 AM, Francisca Ferreira wrote:
>
> External Email - Use Caution
> Dear Experts,
>
> I have extracted subcortical vols corrected for intracranial vols using
> asegstats2table and I  ran mri_glmfit using the following command
>
> mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C
> groupdiff.mtx \--glmdir aseg.glmdir
>
> this seems to have worked.
> I am now trying to visualise my results adapting the recommended wiki
> command
>
> freeview -f
> /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5
> -viewport 3d
>
> Freeview crashes and I'm getting the following error
>
> Number of vertices in overlay data (64 or 64) does not match with surface
> (163842).
> Number of vertices in overlay data (64 or 64) does not match with surface
> (163842).
>
> Is there something wrong with the commands priot  to this step?
>
>
>
>
>
>
>
>
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Re: [Freesurfer] (no subject)

[Douglas N. Greve]

How did you create the sig.mgh that you are trying to overlay?

On 5/28/2021 11:16 AM, Francisca Ferreira wrote:


External Email - Use Caution

Dear Experts,

I have extracted subcortical vols corrected for intracranial vols 
using asegstats2table and I  ran mri_glmfit using the following command


mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C 
groupdiff.mtx \--glmdir aseg.glmdir


this seems to have worked.
I am now trying to visualise my results adapting the recommended wiki 
command


freeview -f 
/usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5 
-viewport 3d


Freeview crashes and I'm getting the following error

Number of vertices in overlay data (64 or 64) does not match with 
surface (163842).
Number of vertices in overlay data (64 or 64) does not match with 
surface (163842).


Is there something wrong with the commands priot  to this step?








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Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

No, you'll have to add it as a covariate. Or you can add --etiv when you run 
mris_preproc and it will divide the maps by the eTIV

On 11/25/2020 3:23 PM, Sara Lyn wrote:

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Hi Freesurfer experts,

I'm doing a surface based volume analysis and wanted to know if there was a 
flag to regress out eTIV in the model.

Thank you



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Re: [Freesurfer] (no subject)

[Douglas N. Greve]

Try this instead
aparcstats2table --hemi lh  --subjects subj10 --parc aparc.a2009s  
--meas meancurv --tablefile /home/team33/ aparcstats.txt


On 11/3/2020 12:20 PM, saman fouladi wrote:


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hi

I run in linux command:
"""
aparcstats2table --hemi lh  --subjects /home/team33/MRI4/subj10/stats 
--parc aparc.a2009s  --meas meancurv --tablefile /home/team33/ 
aparcstats.txt

"""
but show below error an i can not solve it nix:

"""
 File "/usr/local/freesurfer/bin/aparcstats2table", line 156
    print 'ERROR: atleast 1 subject must be provided'
"""

I changed the code several times, but in all cases there is this error.
This error also happens to asegstats2table.

please help me




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Re: [Freesurfer] (no subject)

[Ammon, William]

Hi Saman,

It looks like with the --subjects flag you are pointing Freesurfer to the stats 
directory within a subject directory (where Freesurfer expects the subject 
directory). aparcstats2table and asegstats2table assume a standard Freesurfer 
directory configuration so try entering just the subject directory (one level 
up from stats) is enough and Freesurfer will know to access the proper stats 
files that you specify. Also try and double check your SUBJECTS_DIR.

Cheers,
Bill

From:  on behalf of saman fouladi 

Reply-To: Freesurfer support list 
Date: Tuesday, November 3, 2020 at 12:24 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] (no subject)


External Email - Use Caution
hi

I run in linux command:
"""
aparcstats2table --hemi lh  --subjects /home/team33/MRI4/subj10/stats --parc 
aparc.a2009s  --meas meancurv --tablefile /home/team33/ aparcstats.txt
"""
but show below error an i can not solve it nix:

"""
 File "/usr/local/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
"""

I changed the code several times, but in all cases there is this error.
This error also happens to asegstats2table.

please help me


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Re: [Freesurfer] (no subject)

[Fischl, Bruce]

Sorry, that is not a question for us but rather for your local sys admin

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of saman fouladi
Sent: Friday, October 23, 2020 6:52 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] (no subject)


External Email - Use Caution
hi

I was running several  putty windows for recond-all MRI pictures.


Some putty were inactived during running.


How can I activate them?








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Re: [Freesurfer] (no subject)

[Douglas N. Greve]

Can you run recon-all again with -debug as the first argument? Send me 
the command line and all the terminal output



On 7/9/2020 2:10 PM, Peka Savayan wrote:


External Email - Use Caution

The file that I sent you is the recon-all.log file.

If copying file 'RB_all_2008-03-26.gca' from another FS version to 
directory /freesurfer-7.1.0/average

will solve my problem?



On Thu, Jul 9, 2020 at 12:30 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


Can you send the recon-all.log file?

On 7/9/2020 1:25 PM, Peka Savayan wrote:


External Email - Use Caution

I can open it. Can you? No permission required to my knowledge.

On Thu, Jul 9, 2020 at 11:53 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Do you have read permission to it?

On 7/8/2020 2:25 PM, Peka Savayan wrote:


External Email - Use Caution

Yes.

On Wed, Jul 8, 2020 at 10:01 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Does that file exist?

On 7/7/2020 8:59 AM, Peka Savayan wrote:


External Email - Use Caution

Dear experts,

I try to run recon-all using FS 7.1.0 on a cluster with
OS CentOS6.

I got the recon-all.log error message:

ERROR: cannot find
/share/apps/freesurfer-7.1.0/average/RB_all_2008-03-26.gca

Thanks for your help.
Sincerely,
Peka

-- 
Peka Christova Savayan, PhD

Assistant Prof. Dept. Neuroscience Univ. Minnesota
Member Center Cognitive Sciences Univ. Minnesota
Graduate program Center Cognitive Sciences Univ. Minnesota
Research Physicist Brain Sciences Center VAHCS

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Assistant Prof. Dept. Neuroscience Univ. Minnesota
Member Center Cognitive Sciences Univ. Minnesota
Graduate program Center Cognitive Sciences Univ. Minnesota
Research Physicist Brain Sciences Center VAHCS

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-- 
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Assistant Prof. Dept. Neuroscience Univ. Minnesota
Member Center Cognitive Sciences Univ. Minnesota
Graduate program Center Cognitive Sciences Univ. Minnesota
Research Physicist Brain Sciences Center VAHCS

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Assistant Prof. Dept. Neuroscience Univ. Minnesota
Member Center Cognitive Sciences Univ. Minnesota
Graduate program Center Cognitive Sciences Univ. Minnesota
Research Physicist Brain Sciences Center VAHCS

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Re: [Freesurfer] (no subject)

[Peka Savayan]

External Email - Use Caution

The file that I sent you is the recon-all.log file.

If copying file 'RB_all_2008-03-26.gca' from another FS version to
directory /freesurfer-7.1.0/average
will solve my problem?



On Thu, Jul 9, 2020 at 12:30 PM Douglas N. Greve 
wrote:

> Can you send the recon-all.log file?
>
> On 7/9/2020 1:25 PM, Peka Savayan wrote:
>
> External Email - Use Caution
> I can open it. Can you? No permission required to my knowledge.
>
> On Thu, Jul 9, 2020 at 11:53 AM Douglas N. Greve 
> wrote:
>
>> Do you have read permission to it?
>>
>> On 7/8/2020 2:25 PM, Peka Savayan wrote:
>>
>> External Email - Use Caution
>> Yes.
>>
>> On Wed, Jul 8, 2020 at 10:01 AM Douglas N. Greve 
>> wrote:
>>
>>> Does that file exist?
>>>
>>> On 7/7/2020 8:59 AM, Peka Savayan wrote:
>>>
>>> External Email - Use Caution
>>> Dear experts,
>>>
>>> I try to run recon-all using FS 7.1.0 on a cluster with OS CentOS6.
>>>
>>> I got the recon-all.log error message:
>>>
>>> ERROR: cannot find
>>> /share/apps/freesurfer-7.1.0/average/RB_all_2008-03-26.gca
>>>
>>> Thanks for your help.
>>> Sincerely,
>>> Peka
>>>
>>> --
>>> Peka Christova Savayan, PhD
>>> Assistant Prof. Dept. Neuroscience Univ. Minnesota
>>> Member Center Cognitive Sciences Univ. Minnesota
>>> Graduate program Center Cognitive Sciences Univ. Minnesota
>>> Research Physicist Brain Sciences Center VAHCS
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> --
>> Peka Christova Savayan, PhD
>> Assistant Prof. Dept. Neuroscience Univ. Minnesota
>> Member Center Cognitive Sciences Univ. Minnesota
>> Graduate program Center Cognitive Sciences Univ. Minnesota
>> Research Physicist Brain Sciences Center VAHCS
>>
>> ___
>> Freesurfer mailing 
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>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
> Peka Christova Savayan, PhD
> Assistant Prof. Dept. Neuroscience Univ. Minnesota
> Member Center Cognitive Sciences Univ. Minnesota
> Graduate program Center Cognitive Sciences Univ. Minnesota
> Research Physicist Brain Sciences Center VAHCS
>
> ___
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> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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-- 
Peka Christova Savayan, PhD
Assistant Prof. Dept. Neuroscience Univ. Minnesota
Member Center Cognitive Sciences Univ. Minnesota
Graduate program Center Cognitive Sciences Univ. Minnesota
Research Physicist Brain Sciences Center VAHCS
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Re: [Freesurfer] (no subject)

[Douglas N. Greve]

Can you send the recon-all.log file?

On 7/9/2020 1:25 PM, Peka Savayan wrote:


External Email - Use Caution

I can open it. Can you? No permission required to my knowledge.

On Thu, Jul 9, 2020 at 11:53 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


Do you have read permission to it?

On 7/8/2020 2:25 PM, Peka Savayan wrote:


External Email - Use Caution

Yes.

On Wed, Jul 8, 2020 at 10:01 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Does that file exist?

On 7/7/2020 8:59 AM, Peka Savayan wrote:


External Email - Use Caution

Dear experts,

I try to run recon-all using FS 7.1.0 on a cluster with OS
CentOS6.

I got the recon-all.log error message:

ERROR: cannot find
/share/apps/freesurfer-7.1.0/average/RB_all_2008-03-26.gca

Thanks for your help.
Sincerely,
Peka

-- 
Peka Christova Savayan, PhD

Assistant Prof. Dept. Neuroscience Univ. Minnesota
Member Center Cognitive Sciences Univ. Minnesota
Graduate program Center Cognitive Sciences Univ. Minnesota
Research Physicist Brain Sciences Center VAHCS

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-- 
Peka Christova Savayan, PhD

Assistant Prof. Dept. Neuroscience Univ. Minnesota
Member Center Cognitive Sciences Univ. Minnesota
Graduate program Center Cognitive Sciences Univ. Minnesota
Research Physicist Brain Sciences Center VAHCS

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--
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Assistant Prof. Dept. Neuroscience Univ. Minnesota
Member Center Cognitive Sciences Univ. Minnesota
Graduate program Center Cognitive Sciences Univ. Minnesota
Research Physicist Brain Sciences Center VAHCS

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Re: [Freesurfer] (no subject)

[Peka Savayan]

External Email - Use Caution

I can open it. Can you? No permission required to my knowledge.

On Thu, Jul 9, 2020 at 11:53 AM Douglas N. Greve 
wrote:

> Do you have read permission to it?
>
> On 7/8/2020 2:25 PM, Peka Savayan wrote:
>
> External Email - Use Caution
> Yes.
>
> On Wed, Jul 8, 2020 at 10:01 AM Douglas N. Greve 
> wrote:
>
>> Does that file exist?
>>
>> On 7/7/2020 8:59 AM, Peka Savayan wrote:
>>
>> External Email - Use Caution
>> Dear experts,
>>
>> I try to run recon-all using FS 7.1.0 on a cluster with OS CentOS6.
>>
>> I got the recon-all.log error message:
>>
>> ERROR: cannot find
>> /share/apps/freesurfer-7.1.0/average/RB_all_2008-03-26.gca
>>
>> Thanks for your help.
>> Sincerely,
>> Peka
>>
>> --
>> Peka Christova Savayan, PhD
>> Assistant Prof. Dept. Neuroscience Univ. Minnesota
>> Member Center Cognitive Sciences Univ. Minnesota
>> Graduate program Center Cognitive Sciences Univ. Minnesota
>> Research Physicist Brain Sciences Center VAHCS
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
> Peka Christova Savayan, PhD
> Assistant Prof. Dept. Neuroscience Univ. Minnesota
> Member Center Cognitive Sciences Univ. Minnesota
> Graduate program Center Cognitive Sciences Univ. Minnesota
> Research Physicist Brain Sciences Center VAHCS
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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-- 
Peka Christova Savayan, PhD
Assistant Prof. Dept. Neuroscience Univ. Minnesota
Member Center Cognitive Sciences Univ. Minnesota
Graduate program Center Cognitive Sciences Univ. Minnesota
Research Physicist Brain Sciences Center VAHCS
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Re: [Freesurfer] (no subject)

[Douglas N. Greve]

Do you have read permission to it?

On 7/8/2020 2:25 PM, Peka Savayan wrote:


External Email - Use Caution

Yes.

On Wed, Jul 8, 2020 at 10:01 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


Does that file exist?

On 7/7/2020 8:59 AM, Peka Savayan wrote:


External Email - Use Caution

Dear experts,

I try to run recon-all using FS 7.1.0 on a cluster with OS CentOS6.

I got the recon-all.log error message:

ERROR: cannot find
/share/apps/freesurfer-7.1.0/average/RB_all_2008-03-26.gca

Thanks for your help.
Sincerely,
Peka

-- 
Peka Christova Savayan, PhD

Assistant Prof. Dept. Neuroscience Univ. Minnesota
Member Center Cognitive Sciences Univ. Minnesota
Graduate program Center Cognitive Sciences Univ. Minnesota
Research Physicist Brain Sciences Center VAHCS

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Assistant Prof. Dept. Neuroscience Univ. Minnesota
Member Center Cognitive Sciences Univ. Minnesota
Graduate program Center Cognitive Sciences Univ. Minnesota
Research Physicist Brain Sciences Center VAHCS

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Re: [Freesurfer] (no subject)

[Peka Savayan]

External Email - Use Caution

Yes.

On Wed, Jul 8, 2020 at 10:01 AM Douglas N. Greve 
wrote:

> Does that file exist?
>
> On 7/7/2020 8:59 AM, Peka Savayan wrote:
>
> External Email - Use Caution
> Dear experts,
>
> I try to run recon-all using FS 7.1.0 on a cluster with OS CentOS6.
>
> I got the recon-all.log error message:
>
> ERROR: cannot find
> /share/apps/freesurfer-7.1.0/average/RB_all_2008-03-26.gca
>
> Thanks for your help.
> Sincerely,
> Peka
>
> --
> Peka Christova Savayan, PhD
> Assistant Prof. Dept. Neuroscience Univ. Minnesota
> Member Center Cognitive Sciences Univ. Minnesota
> Graduate program Center Cognitive Sciences Univ. Minnesota
> Research Physicist Brain Sciences Center VAHCS
>
> ___
> Freesurfer mailing 
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>
>
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-- 
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Assistant Prof. Dept. Neuroscience Univ. Minnesota
Member Center Cognitive Sciences Univ. Minnesota
Graduate program Center Cognitive Sciences Univ. Minnesota
Research Physicist Brain Sciences Center VAHCS


100206_FS.o41703
Description: Binary data
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Re: [Freesurfer] (no subject)

[Douglas N. Greve]

Does that file exist?

On 7/7/2020 8:59 AM, Peka Savayan wrote:


External Email - Use Caution

Dear experts,

I try to run recon-all using FS 7.1.0 on a cluster with OS CentOS6.

I got the recon-all.log error message:

ERROR: cannot find 
/share/apps/freesurfer-7.1.0/average/RB_all_2008-03-26.gca


Thanks for your help.
Sincerely,
Peka

--
Peka Christova Savayan, PhD
Assistant Prof. Dept. Neuroscience Univ. Minnesota
Member Center Cognitive Sciences Univ. Minnesota
Graduate program Center Cognitive Sciences Univ. Minnesota
Research Physicist Brain Sciences Center VAHCS

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Re: [Freesurfer] Which subject does recon-all register surfaces to?

[Ian Hardingham]

   External Email - Use Caution


Thanks Bruce.

On 13/05/2020 15:41, Bruce Fischl wrote:

Hi Ian

we don't register to an individual subject - we register to a 
probabilistic atlas compiled from many subjects. The fsaverage 
subjects were also generated from that data so they are in register, 
but the actual atlas is a .tif file that you can find as the target of 
mris_register in your recon-all.log file


cheers
Bruce


On Wed, 13 May 2020, Ian wrote:



External Email - Use Caution

Hi guys.

After recon-all, the /surf/?h.sphere.reg file implies a registration has
been performed to an "average" subject on a sphere.  Can you please 
tell me

which subject this is?  Is it SUBJECTS_DIR/fsaverage?  If so, what is
SUBJECTS_DIR/fsaverage/lh.sphere.reg a registration to?  If not, 
where can I

find the subject that recon-all registers to?

Thanks,

Ian

--

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Re: [Freesurfer] Which subject does recon-all register surfaces to?

[Bruce Fischl]

Hi Ian

we don't register to an individual subject - we register to a 
probabilistic atlas compiled from many subjects. The fsaverage subjects 
were also generated from that data so they are in register, but the actual 
atlas is a .tif file that you can find as the target of mris_register in 
your recon-all.log file


cheers
Bruce


On Wed, 13 May 
2020, Ian wrote:




External Email - Use Caution

Hi guys.

After recon-all, the /surf/?h.sphere.reg file implies a registration has
been performed to an "average" subject on a sphere.  Can you please tell me
which subject this is?  Is it SUBJECTS_DIR/fsaverage?  If so, what is
SUBJECTS_DIR/fsaverage/lh.sphere.reg a registration to?  If not, where can I
find the subject that recon-all registers to?

Thanks,

Ian

--

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Re: [Freesurfer] (No Subject)

[KennethSPrice]

External Email - Use Caution

is there a way to visualize the changes in thickness, area, and volume between 
the 2 timepoints (cortical and subcortical)? I was under the impression that 
running mri_preproc would aloow me to visualize change in cortical thickness bt 
the 2 timepoints (lh.paired.thickness.mgh).

Sent with [ProtonMail](https://protonmail.com) Secure Email.

‐‐‐ Original Message ‐‐‐
On Friday, May 1, 2020 12:14 PM, Douglas N. Greve  
wrote:

> Oh, right. You only have one data point (the difference) and you are 
> computing one parameter (the mean), so you have 0 DOF. If you only have one 
> data point, there are not statistical tests you can do
>
> On 5/1/2020 3:34 AM, KennethSPrice wrote:
>
>> External Email - Use Caution
>>
>> In the FSGD file I have one subject pair (timepoint 1 and timepoint 2), and 
>> it is the only group. However, I removed --fsgd and replaced it with --osgm 
>> upon your reccomendation, and am still getting the error.
>>
>> I am also having an issue visualizing the output of mri_preproc in freeview 
>> - isnt this mgh file supposed to be a volume? Is there a way to center the 
>> freeview cursor to the middle of the current volume?
>>
>> Thanks,
>> Ken
>>
>> ‐‐‐ Original Message ‐‐‐
>> On Thursday, April 30, 2020 2:16 PM, Douglas N. Greve 
>>  wrote:
>>
>>> how many subjects are there in your fsgd? How many groups in your fsgd 
>>> file? Also, you should not use --osgm and --fsgd
>>>
>>> On 4/30/2020 1:09 PM, KennethSPrice wrote:
>>>
 External Email - Use Caution

 Hello Freesurfer friends!

 I'm going through the "paired analysis" tutorial and am running into an 
 issue with the mri_glmfit. I am running on just one subject pair. 
 https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit

 I ran mris_preproc on my 2 timepoints and am getting an error at mri_glmfit

 mris_preproc --target fsaverage --hemi lh \
--meas thickness --out lh.paired-diff.thickness.mgh \
--fsgd pairs.fsgd --paired-diff

 mri_glmfit \
  --glmdir lh.paired-diff \
  --y lh.paired-diff.thickness.sm05.mgh \
  --fsgd paired-diff.fsgd \

 --osgm \

 --surf fsaverage lh

 I am getting an ERROR: DOF = 0.

 MRI's have been put through recon-all and are in there own directories 
 within SUBJECTS_DIR.

 What is the cause of the error?

 Thanks,

 Ken

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Re: [Freesurfer] (No Subject)

[Douglas N. Greve]

For thickness, you can look at the difference (or percent difference). 
You would use freeview (or tksurferfv, which is a frontend for 
freeview). When you run mris_preproc, you can specify that you want it 
to compute the (percent) difference, or you can do it with the 
multi-frame output of mris_preproc. For subcortical, it is more 
difficult since you don't get a map out of it (just a single value like 
total volume of hippocampus).



On 5/11/2020 3:52 PM, KennethSPrice wrote:


External Email - Use Caution

is there a way to visualize the changes in thickness, area, and volume 
between the 2 timepoints (cortical and subcortical)? I was under the 
impression that running mri_preproc would aloow me to visualize change 
in cortical thickness bt the 2 timepoints (lh.paired.thickness.mgh).



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‐‐‐ Original Message ‐‐‐
On Friday, May 1, 2020 12:14 PM, Douglas N. Greve 
 wrote:


Oh, right. You only have one data point (the difference) and you are 
computing one parameter (the mean), so you have 0 DOF. If you only 
have one data point, there are not statistical tests you can do



On 5/1/2020 3:34 AM, KennethSPrice wrote:


*External Email - Use Caution *


In the FSGD file I have one subject pair (timepoint 1 and timepoint 
2), and it is the only group. However, I removed --fsgd and replaced 
it with --osgm upon your reccomendation, and am still getting the error.


I am also having an issue visualizing the output of mri_preproc in 
freeview - isnt this mgh file supposed to be a volume? Is there a 
way to center the freeview cursor to the middle of the current volume?


Thanks,
Ken



‐‐‐ Original Message ‐‐‐
On Thursday, April 30, 2020 2:16 PM, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


how many subjects are there in your fsgd? How many groups in your 
fsgd file? Also, you should not use --osgm and --fsgd



On 4/30/2020 1:09 PM, KennethSPrice wrote:


*External Email - Use Caution *

Hello Freesurfer friends!

I'm going through the "paired analysis" tutorial and am running 
into an issue with the mri_glmfit. I am running on just one 
subject pair. 
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit


I ran mris_preproc on my 2 timepoints and am getting an error at 
mri_glmfit

   mris_preproc --target fsaverage --hemi lh \
--meas thickness --out lh.paired-diff.thickness.mgh \
--fsgd pairs.fsgd --paired-diff



mri_glmfit \
  --glmdir lh.paired-diff \
  --y lh.paired-diff.thickness.sm05.mgh \
  --fsgd paired-diff.fsgd \


--osgm \


--surf fsaverage lh


I am getting an ERROR: DOF = 0.


MRI's have been put through recon-all and are in there own directories within 
SUBJECTS_DIR.


What is the cause of the error?


Thanks,


Ken


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Cleveland Clinic is currently ranked as one of the nation’s top 
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message is intended for use only by the individual or entity to 
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Re: [Freesurfer] (No Subject)

[Douglas N. Greve]

Oh, right. You only have one data point (the difference) and you are 
computing one parameter (the mean), so you have 0 DOF. If you only have 
one data point, there are not statistical tests you can do


On 5/1/2020 3:34 AM, KennethSPrice wrote:


External Email - Use Caution


In the FSGD file I have one subject pair (timepoint 1 and timepoint 
2), and it is the only group. However, I removed --fsgd and replaced 
it with --osgm upon your reccomendation, and am still getting the error.


I am also having an issue visualizing the output of mri_preproc in 
freeview - isnt this mgh file supposed to be a volume? Is there a way 
to center the freeview cursor to the middle of the current volume?


Thanks,
Ken



‐‐‐ Original Message ‐‐‐
On Thursday, April 30, 2020 2:16 PM, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


how many subjects are there in your fsgd? How many groups in your 
fsgd file? Also, you should not use --osgm and --fsgd



On 4/30/2020 1:09 PM, KennethSPrice wrote:


*External Email - Use Caution *

Hello Freesurfer friends!

I'm going through the "paired analysis" tutorial and am running into 
an issue with the mri_glmfit. I am running on just one subject pair. 
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit


I ran mris_preproc on my 2 timepoints and am getting an error at 
mri_glmfit

   mris_preproc --target fsaverage --hemi lh \
--meas thickness --out lh.paired-diff.thickness.mgh \
--fsgd pairs.fsgd --paired-diff


mri_glmfit \
  --glmdir lh.paired-diff \
  --y lh.paired-diff.thickness.sm05.mgh \
  --fsgd paired-diff.fsgd \

--osgm \

--surf fsaverage lh

I am getting an ERROR: DOF = 0.

MRI's have been put through recon-all and are in there own directories within 
SUBJECTS_DIR.

What is the cause of the error?

Thanks,

Ken

Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as one of the nation’s top 
hospitals by /U.S. News & World Report/ (2019-2020). Visit us online 
at http://www.clevelandclinic.org for a complete listing of our 
services, staff and locations. Confidentiality Note: This message is 
intended for use only by the individual or entity to which it is 
addressed and may contain information that is privileged, 
confidential, and exempt from disclosure under applicable law. If 
the reader of this message is not the intended recipient or the 
employee or agent responsible for delivering the message to the 
intended recipient, you are hereby notified that any dissemination, 
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prohibited. If you have received this communication in error, please 
contact the sender immediately and destroy the material in its 
entirety, whether electronic or hard copy. Thank you.



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Re: [Freesurfer] (No Subject)

[KennethSPrice]

External Email - Use Caution

In the FSGD file I have one subject pair (timepoint 1 and timepoint 2), and it 
is the only group. However, I removed --fsgd and replaced it with --osgm upon 
your reccomendation, and am still getting the error.

I am also having an issue visualizing the output of mri_preproc in freeview - 
isnt this mgh file supposed to be a volume? Is there a way to center the 
freeview cursor to the middle of the current volume?

Thanks,
Ken

‐‐‐ Original Message ‐‐‐
On Thursday, April 30, 2020 2:16 PM, Douglas N. Greve  
wrote:

> how many subjects are there in your fsgd? How many groups in your fsgd file? 
> Also, you should not use --osgm and --fsgd
>
> On 4/30/2020 1:09 PM, KennethSPrice wrote:
>
>> External Email - Use Caution
>>
>> Hello Freesurfer friends!
>>
>> I'm going through the "paired analysis" tutorial and am running into an 
>> issue with the mri_glmfit. I am running on just one subject pair. 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit
>>
>> I ran mris_preproc on my 2 timepoints and am getting an error at mri_glmfit
>>
>> mris_preproc --target fsaverage --hemi lh \
>>--meas thickness --out lh.paired-diff.thickness.mgh \
>>--fsgd pairs.fsgd --paired-diff
>>
>> mri_glmfit \
>>  --glmdir lh.paired-diff \
>>  --y lh.paired-diff.thickness.sm05.mgh \
>>  --fsgd paired-diff.fsgd \
>>
>> --osgm \
>>
>> --surf fsaverage lh
>>
>> I am getting an ERROR: DOF = 0.
>>
>> MRI's have been put through recon-all and are in there own directories 
>> within SUBJECTS_DIR.
>>
>> What is the cause of the error?
>>
>> Thanks,
>>
>> Ken
>>
>> Please consider the environment before printing this e-mail
>>
>> Cleveland Clinic is currently ranked as one of the nation’s top hospitals by 
>> U.S. News & World Report (2019-2020). Visit us online at 
>> http://www.clevelandclinic.org for a complete listing of our services, staff 
>> and locations. Confidentiality Note: This message is intended for use only 
>> by the individual or entity to which it is addressed and may contain 
>> information that is privileged, confidential, and exempt from disclosure 
>> under applicable law. If the reader of this message is not the intended 
>> recipient or the employee or agent responsible for delivering the message to 
>> the intended recipient, you are hereby notified that any dissemination, 
>> distribution or copying of this communication is strictly prohibited. If you 
>> have received this communication in error, please contact the sender 
>> immediately and destroy the material in its entirety, whether electronic or 
>> hard copy. Thank you.
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___
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Re: [Freesurfer] (No Subject)

[Douglas N. Greve]

how many subjects are there in your fsgd? How many groups in your fsgd 
file? Also, you should not use --osgm and --fsgd


On 4/30/2020 1:09 PM, KennethSPrice wrote:


External Email - Use Caution

Hello Freesurfer friends!

I'm going through the "paired analysis" tutorial and am running into 
an issue with the mri_glmfit. I am running on just one subject pair. 
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit


I ran mris_preproc on my 2 timepoints and am getting an error at 
mri_glmfit

   mris_preproc --target fsaverage --hemi lh \
--meas thickness --out lh.paired-diff.thickness.mgh \
--fsgd pairs.fsgd --paired-diff

mri_glmfit \
  --glmdir lh.paired-diff \
  --y lh.paired-diff.thickness.sm05.mgh \
  --fsgd paired-diff.fsgd \
--osgm \
--surf fsaverage lh
I am getting an ERROR: DOF = 0.
MRI's have been put through recon-all and are in there own directories within 
SUBJECTS_DIR.
What is the cause of the error?
Thanks,
Ken

Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as one of the nation’s top 
hospitals by /U.S. News & World Report/ (2019-2020). Visit us online 
at http://www.clevelandclinic.org for a complete listing of our 
services, staff and locations. Confidentiality Note: This message is 
intended for use only by the individual or entity to which it is 
addressed and may contain information that is privileged, 
confidential, and exempt from disclosure under applicable law. If the 
reader of this message is not the intended recipient or the employee 
or agent responsible for delivering the message to the intended 
recipient, you are hereby notified that any dissemination, 
distribution or copying of this communication is strictly prohibited. 
If you have received this communication in error, please contact the 
sender immediately and destroy the material in its entirety, whether 
electronic or hard copy. Thank you.



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Re: [Freesurfer] (no subject)

[Paul Wighton]

External Email - Use Caution

Hi Aleksandr,

You could try making a minimal container with reprozip
https://www.reprozip.org/

Only recon-all should be less than a Gb.

-Paul


On Wed, Apr 22, 2020 at 5:31 PM Hoopes, Andrew 
wrote:

> I don’t have an exact number, but I believe the minimal compiled
> distribution is less than 2GB.
>
> Andrew
>
>
>
> *From: * on behalf of Ерохин
> Александр 
> *Reply-To: *Ерохин Александр , FS Help <
> freesurfer@nmr.mgh.harvard.edu>
> *Date: *Wednesday, April 22, 2020 at 12:35 PM
> *To: *FS Help 
> *Subject: *Re: [Freesurfer] (no subject)
>
>
>
> *External Email - Use Caution*
>
> Hi Andrew,
>
>
>
> Alright, many thanks for the hint! I started experimenting myself with
> file exclusion, but is seems I've excluded too much and recon-all is not
> able to complete successfully anymore.
>
>
>
> Regarding this MINIMAL flag option — could you please tell an approximate
> distribution size with it is specified?
>
> Does it worth the trouble?
>
>
>
> Regards,
>
> Aleksandr.
>
>
>
>
>
> Понедельник, 20 апреля 2020, 19:36 +03:00 от "Hoopes, Andrew" <
> ahoo...@mgh.harvard.edu>:
>
>
> Hi Aleksandr,
>
>
>
> Yes, this is an unfortunate limitation, but we are working towards making
> freesurfer more modular in the future. There’s no single straightforward
> solution to cutting down the distribution, but you do have a couple of
> options.
>
>
>
> The BIDS group has created a minimal FS6 docker container that removes a
> lot of unnecessary subject data for recon-all. Their dockerfile is
> available at
> https://github.com/BIDS-Apps/freesurfer/blob/master/Dockerfile and you
> can mimic that second wget command to download a filtered version of FS.
>
>
>
> Also, if you’re familiar with the development process, you can build your
> own freesurfer distribution following the instructions at
> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildGuide. There is a cmake
> flag `MINIMAL` that will only build core recon-all components if it is set
> to ON. This is a more complete option than the first, but also much more
> time consuming…
>
>
>
> Hope that helps,
>
> Andrew Hoopes
>
>
>
> *From: * on behalf of Ерохин
> Александр 
> *Reply-To: *Ерохин Александр , FS Help <
> freesurfer@nmr.mgh.harvard.edu>
> *Date: *Sunday, April 19, 2020 at 1:49 PM
> *To: *FS Help 
> *Subject: *[Freesurfer] (no subject)
>
>
>
> *External Email - Use Caution*
>
> Hello together,
>
>
>
> The FreeSurfer distribution takes * 10G* of the disk space in my local
> installation. It has numerous tools, but it’s not modular, or at lest it’s
> very hard to tell boundaries between modules.
>
>
>
> E.g. /bin folder contains around 860 executables all in one place.
>
>
>
> Is it possible to trim down the distribution provided to minimize the size
> but keep it functional in terms of computation for *recon-all* steps?
>
> For example trim away all GUI executables and support libraries.
>
>
>
> As far as I can see, the directories taking most of the space are:
>
>
>
> 2.2G*./subjects*
> 3.1G*./average*
> 2.5G*./bin*
> 1.3G*./lib*
>
>
>
> But I am not sure what could be removed and what not in order to keep all
> recon-all steps functional.
>
>
>
> Many thanks,
>
> Aleksandr.
>
>
>
>
>
> ___
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>
>
>
>
>
>
>
>
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Re: [Freesurfer] (no subject)

[Hoopes, Andrew]

I don’t have an exact number, but I believe the minimal compiled distribution 
is less than 2GB.
Andrew

From:  on behalf of Ерохин Александр 

Reply-To: Ерохин Александр , FS Help 

Date: Wednesday, April 22, 2020 at 12:35 PM
To: FS Help 
Subject: Re: [Freesurfer] (no subject)


External Email - Use Caution
Hi Andrew,

Alright, many thanks for the hint! I started experimenting myself with file 
exclusion, but is seems I've excluded too much and recon-all is not able to 
complete successfully anymore.

Regarding this MINIMAL flag option — could you please tell an approximate 
distribution size with it is specified?
Does it worth the trouble?

Regards,
Aleksandr.


Понедельник, 20 апреля 2020, 19:36 +03:00 от "Hoopes, Andrew" 
:


Hi Aleksandr,



Yes, this is an unfortunate limitation, but we are working towards making 
freesurfer more modular in the future. There’s no single straightforward 
solution to cutting down the distribution, but you do have a couple of options.



The BIDS group has created a minimal FS6 docker container that removes a lot of 
unnecessary subject data for recon-all. Their dockerfile is available at 
https://github.com/BIDS-Apps/freesurfer/blob/master/Dockerfile and you can 
mimic that second wget command to download a filtered version of FS.



Also, if you’re familiar with the development process, you can build your own 
freesurfer distribution following the instructions at 
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildGuide. There is a cmake flag 
`MINIMAL` that will only build core recon-all components if it is set to ON. 
This is a more complete option than the first, but also much more time 
consuming…



Hope that helps,

Andrew Hoopes



From: 
>
 on behalf of Ерохин Александр 
>
Reply-To: Ерохин Александр 
>, FS Help 
>
Date: Sunday, April 19, 2020 at 1:49 PM
To: FS Help 
>
Subject: [Freesurfer] (no subject)



External Email - Use Caution

Hello together,



The FreeSurfer distribution takes 10G of the disk space in my local 
installation. It has numerous tools, but it’s not modular, or at lest it’s very 
hard to tell boundaries between modules.



E.g. /bin folder contains around 860 executables all in one place.



Is it possible to trim down the distribution provided to minimize the size but 
keep it functional in terms of computation for recon-all steps?

For example trim away all GUI executables and support libraries.



As far as I can see, the directories taking most of the space are:



2.2G./subjects
3.1G./average
2.5G./bin
1.3G./lib



But I am not sure what could be removed and what not in order to keep all 
recon-all steps functional.



Many thanks,

Aleksandr.




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Re: [Freesurfer] (no subject)

[Ерохин Александр]

External Email - Use Caution

Hi Andrew,
 
Alright, many thanks for the hint! I started experimenting myself with file 
exclusion, but is seems I've excluded too much and recon-all is not able to 
complete successfully anymore.
 
Regarding this MINIMAL flag option — could you please tell an approximate 
distribution size with it is specified?
Does it worth the trouble?
 
Regards,
Aleksandr.
 
  
>Понедельник, 20 апреля 2020, 19:36 +03:00 от "Hoopes, Andrew" 
>:
> 
>Hi Aleksandr,
> 
>Yes, this is an unfortunate limitation, but we are working towards making 
>freesurfer more modular in the future. There’s no single straightforward 
>solution to cutting down the distribution, but you do have a couple of options.
> 
>The BIDS group has created a minimal FS6 docker container that removes a lot 
>of unnecessary subject data for recon-all. Their dockerfile is available at  
>https://github.com/BIDS-Apps/freesurfer/blob/master/Dockerfile and you can 
>mimic that second wget command to download a filtered version of FS.
> 
>Also, if you’re familiar with the development process, you can build your own 
>freesurfer distribution following the instructions at  
>https://surfer.nmr.mgh.harvard.edu/fswiki/BuildGuide . There is a cmake flag 
>`MINIMAL` that will only build core recon-all components if it is set to ON. 
>This is a more complete option than the first, but also much more time 
>consuming…
> 
>Hope that helps,
>Andrew Hoopes
> 
>From:  < freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Ерохин 
>Александр < erohin_...@mail.ru >
>Reply-To:  Ерохин Александр < erohin_...@mail.ru >, FS Help < 
>freesurfer@nmr.mgh.harvard.edu >
>Date:  Sunday, April 19, 2020 at 1:49 PM
>To:  FS Help < freesurfer@nmr.mgh.harvard.edu >
>Subject:  [Freesurfer] (no subject)
> 
>External Email - Use Caution
>Hello together,
> 
>The FreeSurfer distribution takes  10G of the disk space in my local 
>installation. It has numerous tools, but it’s not modular, or at lest it’s 
>very hard to tell boundaries between modules.
> 
>E.g. /bin folder contains around 860 executables all in one place.
> 
>Is it possible to trim down the distribution provided to minimize the size but 
>keep it functional in terms of computation for  recon-all steps?
>For example trim away all GUI executables and support libraries.
> 
>As far as I can see, the directories taking most of the space are:
> 
>2.2G     ./subjects
>3.1G     ./average
>2.5G     ./bin
>1.3G     ./lib
> 
>But I am not sure what could be removed and what not in order to keep all 
>recon-all steps functional.
> 
>Many thanks,
>Aleksandr.
> 
> 
>___
>Freesurfer mailing list
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Re: [Freesurfer] (no subject)

[Hoopes, Andrew]

Hi Aleksandr,

Yes, this is an unfortunate limitation, but we are working towards making 
freesurfer more modular in the future. There’s no single straightforward 
solution to cutting down the distribution, but you do have a couple of options.

The BIDS group has created a minimal FS6 docker container that removes a lot of 
unnecessary subject data for recon-all. Their dockerfile is available at 
https://github.com/BIDS-Apps/freesurfer/blob/master/Dockerfile and you can 
mimic that second wget command to download a filtered version of FS.

Also, if you’re familiar with the development process, you can build your own 
freesurfer distribution following the instructions at 
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildGuide. There is a cmake flag 
`MINIMAL` that will only build core recon-all components if it is set to ON. 
This is a more complete option than the first, but also much more time 
consuming…

Hope that helps,
Andrew Hoopes

From:  on behalf of Ерохин Александр 

Reply-To: Ерохин Александр , FS Help 

Date: Sunday, April 19, 2020 at 1:49 PM
To: FS Help 
Subject: [Freesurfer] (no subject)


External Email - Use Caution
Hello together,

The FreeSurfer distribution takes 10G of the disk space in my local 
installation. It has numerous tools, but it’s not modular, or at lest it’s very 
hard to tell boundaries between modules.

E.g. /bin folder contains around 860 executables all in one place.

Is it possible to trim down the distribution provided to minimize the size but 
keep it functional in terms of computation for recon-all steps?
For example trim away all GUI executables and support libraries.

As far as I can see, the directories taking most of the space are:

2.2G./subjects
3.1G./average
2.5G./bin
1.3G./lib

But I am not sure what could be removed and what not in order to keep all 
recon-all steps functional.

Many thanks,
Aleksandr.


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Re: [Freesurfer] (no subject)

[Peng Liu]

External Email - Use Caution

Thank you so much. I shall modify my other scripts then.

Peng


On Mon, 6 Apr 2020 at 16:59, Ruopeng Wang 
wrote:

> I don’t think look up table works with negative indices. It was mainly
> designed for label volumes.
>
> Ruopeng
>
> On Apr 6, 2020, at 10:35 AM, Peng Liu  wrote:
>
> External Email - Use Caution
>
> Hi Ruopeng,
>
> Thank you for your reply.
>
> I have also tried NIH and JET, but with negative scale, the entire image
> will turn into one same color as if there is some error.
>
> Meanwhile the reason of me trying to create .lut map is because I want
> five colours and five colours only...
>
> Is there any specific reason to not display negative scales with look up
> table? Will it cause any error or jeopardize the results displayed?
>
> Many Thanks
>
> Peng
>
>
> On Mon, 6 Apr 2020 at 16:13, Ruopeng Wang 
> wrote:
>
>> Hi Peng,
>>
>> Your lookup table only contains indices between 0 to 6. In any case I
>> would not use look up table to display negative scales. Have you tried any
>> other color maps like JET or NIH which has more colors?
>>
>> Best,
>> Ruopeng
>>
>> On Apr 6, 2020, at 6:30 AM, Peng Liu  wrote:
>>
>> External Email - Use Caution
>>
>> Dear Freesurfer experts,
>>
>> I am trying to customize a colour map of my own, with five colours and
>> scale from -12.5 to 12.5, since when using Heat (with default options), the
>> scale is correct but it is shown in only four colours.
>>
>> However after I created the .lut file (attached below), when loading it
>> into freeview, the colour scale is from 0 to 6.
>>
>> 
>>
>> Does this mean I should also include scale information in the .lut file?
>>
>> Any help would be much appreciated.
>>
>> Peng Liu
>> ___
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>>
>>
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Re: [Freesurfer] (no subject)

[Ruopeng Wang]

I don’t think look up table works with negative indices. It was mainly designed 
for label volumes. 

Ruopeng

> On Apr 6, 2020, at 10:35 AM, Peng Liu  wrote:
> 
> External Email - Use Caution
> 
> 
> Hi Ruopeng,
> 
> Thank you for your reply.
> 
> I have also tried NIH and JET, but with negative scale, the entire image will 
> turn into one same color as if there is some error.
> 
> Meanwhile the reason of me trying to create .lut map is because I want five 
> colours and five colours only...
> 
> Is there any specific reason to not display negative scales with look up 
> table? Will it cause any error or jeopardize the results displayed?
> 
> Many Thanks
> 
> Peng
> 
> 
> On Mon, 6 Apr 2020 at 16:13, Ruopeng Wang  > wrote:
> Hi Peng,
> 
> Your lookup table only contains indices between 0 to 6. In any case I would 
> not use look up table to display negative scales. Have you tried any other 
> color maps like JET or NIH which has more colors?
> 
> Best,
> Ruopeng
> 
>> On Apr 6, 2020, at 6:30 AM, Peng Liu > > wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> Dear Freesurfer experts,
>> 
>> I am trying to customize a colour map of my own, with five colours and scale 
>> from -12.5 to 12.5, since when using Heat (with default options), the scale 
>> is correct but it is shown in only four colours.
>> 
>> However after I created the .lut file (attached below), when loading it into 
>> freeview, the colour scale is from 0 to 6.
>> 
>> 
>> 
>> Does this mean I should also include scale information in the .lut file?
>> 
>> Any help would be much appreciated.
>> 
>> Peng Liu
>> ___
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>> 
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Re: [Freesurfer] (no subject)

[Peng Liu]

External Email - Use Caution

Hi Ruopeng,

Thank you for your reply.

I have also tried NIH and JET, but with negative scale, the entire image
will turn into one same color as if there is some error.

Meanwhile the reason of me trying to create .lut map is because I want five
colours and five colours only...

Is there any specific reason to not display negative scales with look up
table? Will it cause any error or jeopardize the results displayed?

Many Thanks

Peng


On Mon, 6 Apr 2020 at 16:13, Ruopeng Wang 
wrote:

> Hi Peng,
>
> Your lookup table only contains indices between 0 to 6. In any case I
> would not use look up table to display negative scales. Have you tried any
> other color maps like JET or NIH which has more colors?
>
> Best,
> Ruopeng
>
> On Apr 6, 2020, at 6:30 AM, Peng Liu  wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I am trying to customize a colour map of my own, with five colours and
> scale from -12.5 to 12.5, since when using Heat (with default options), the
> scale is correct but it is shown in only four colours.
>
> However after I created the .lut file (attached below), when loading it
> into freeview, the colour scale is from 0 to 6.
>
> 
>
> Does this mean I should also include scale information in the .lut file?
>
> Any help would be much appreciated.
>
> Peng Liu
> ___
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>
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Re: [Freesurfer] (no subject)

[Ruopeng Wang]

Hi Peng,

Your lookup table only contains indices between 0 to 6. In any case I would not 
use look up table to display negative scales. Have you tried any other color 
maps like JET or NIH which has more colors?

Best,
Ruopeng

> On Apr 6, 2020, at 6:30 AM, Peng Liu  wrote:
> 
> External Email - Use Caution
> 
> 
> Dear Freesurfer experts,
> 
> I am trying to customize a colour map of my own, with five colours and scale 
> from -12.5 to 12.5, since when using Heat (with default options), the scale 
> is correct but it is shown in only four colours.
> 
> However after I created the .lut file (attached below), when loading it into 
> freeview, the colour scale is from 0 to 6.
> 
> 
> 
> Does this mean I should also include scale information in the .lut file?
> 
> Any help would be much appreciated.
> 
> Peng Liu
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] within-subject contrast between runs

[Douglas N. Greve]

In par file for the A run, you say that the condition number is 1; in 
the par file for run B, say that the condition is number 2 (so condition 
2 does not appear in run 1's parfile, and condition 1 does not appear in 
run 2's). The in mkcontrast-sess, just select -a 1 -c 2



On 3/11/2020 1:42 PM, Milde, Christopher wrote:


External Email - Use Caution

Dear Mr. Greve


Thanks for your suggestions.


However I'm still a bit puzzled about how to contrast two runs 
corresponding to different stimulations (StimA: runA and StimB:runB) 
from one subject.


I have two runs each containing a paradigm file corresponding to one 
of the two stimulations.


How is it possible to contrast those two stimulation conditions 
acquired in two different runs since one run and thus also the 
paradigm file does not contain both stimulation conditions?


Seemingly both stimulation conditions must be in one paradigm file set 
to different onset timings to perform mkcontrast-sess



My folder Structure is as follows

Project Name

Session = Subject

Runs (001, 002) = Stimulation A and Stimulation B, each with a 
separate paradigm file



I know that I do not have to model the no-stimulation periods explicitely


Best wishes

Chris


*Von:* freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. 
Greve 

*Gesendet:* Freitag, 6. März 2020 17:54:16
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] within-subject contrast between runs


On 3/6/2020 11:15 AM, Milde, Christopher wrote:


External Email - Use Caution

Dear Freesurfer Experts,


I have a very basic questions about creating subject-wise contrasts 
between runs


*
*

*Background*

Study with two runs per subject where each run corresponds two a 
different condition (i.e. Stimulation A (on - off) and Stimulation B 
(on - off).


I performed the preprocessing and 1st levels stats in the native 
subjects space



*Questions*

  * How can I obtain a within-subjects contrast between two runs (the
Stimulation A vs. Stimulation B ) obtained in two runs within one
session?

The easiest way is to code the conditions differently in the paradigm 
file (eg, instead of two conditions, you'd have 4, ARun1, BRun1, 
ARun2, BRun2), then just create contrasts as normal


  * Can I obtain this within-subject contrast by staying in the
native subject space?

It can be done in fsaverage or the native subject surface space, it is 
not related.


  * Do I have to concatenate both runs and create a new parradigm file?


No, see above



Thanks for your support


Sincerely

Chris




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Re: [Freesurfer] within-subject contrast between runs

[Milde, Christopher]

External Email - Use Caution

Dear Mr. Greve


Thanks for your suggestions.


However I'm still a bit puzzled about how to contrast two runs corresponding to 
different stimulations (StimA: runA and StimB:runB) from one subject.

I have two runs each containing a paradigm file corresponding to one of the two 
stimulations.

How is it possible to contrast those two stimulation conditions acquired in two 
different runs since one run and thus also the paradigm file does not contain 
both stimulation conditions?

Seemingly both stimulation conditions must be in one paradigm file set to 
different onset timings to perform mkcontrast-sess


My folder Structure is as follows

Project Name

Session = Subject

Runs (001, 002) = Stimulation A and Stimulation B, each with a separate 
paradigm file


I know that I do not have to model the no-stimulation periods explicitely


Best wishes

Chris


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. Greve 

Gesendet: Freitag, 6. März 2020 17:54:16
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] within-subject contrast between runs



On 3/6/2020 11:15 AM, Milde, Christopher wrote:

External Email - Use Caution

Dear Freesurfer Experts,


I have a very basic questions about creating subject-wise contrasts between runs



Background

Study with two runs per subject where each run corresponds two a different 
condition (i.e. Stimulation A (on - off) and Stimulation B (on - off).

I performed the preprocessing and 1st levels stats in the native subjects space


Questions

  *   How can I obtain a within-subjects contrast between two runs (the 
Stimulation A vs. Stimulation B )  obtained in two runs within one session?

The easiest way is to code the conditions differently in the paradigm file (eg, 
instead of two conditions, you'd have 4, ARun1, BRun1, ARun2, BRun2), then just 
create contrasts as normal

  *   Can I obtain this within-subject contrast by staying in the native 
subject space?

It can be done in fsaverage or the native subject surface space, it is not 
related.

  *   Do I have to concatenate both runs and create a new parradigm file?

No, see above


Thanks for your support


Sincerely

Chris





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Re: [Freesurfer] within-subject contrast between runs

[Douglas N. Greve]

On 3/6/2020 11:15 AM, Milde, Christopher wrote:


External Email - Use Caution

Dear Freesurfer Experts,


I have a very basic questions about creating subject-wise contrasts 
between runs


*
*

*Background*

Study with two runs per subject where each run corresponds two a 
different condition (i.e. Stimulation A (on - off) and Stimulation B 
(on - off).


I performed the preprocessing and 1st levels stats in the native 
subjects space



*Questions*

  * How can I obtain a within-subjects contrast between two runs (the
Stimulation A vs. Stimulation B )  obtained in two runs within one
session?

The easiest way is to code the conditions differently in the paradigm 
file (eg, instead of two conditions, you'd have 4, ARun1, BRun1, ARun2, 
BRun2), then just create contrasts as normal


  * Can I obtain this within-subject contrast by staying in the native
subject space?

It can be done in fsaverage or the native subject surface space, it is 
not related.


  * Do I have to concatenate both runs and create a new parradigm file?


No, see above



Thanks for your support


Sincerely

Chris




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Re: [Freesurfer] (no subject)

[Douglas N. Greve]

It is is really bright there, try putting a few control points in WM 
(make sure they are in WM)

On 3/3/20 12:30 PM, Laboratorio de Neurociencia Funcional wrote:
>
> External Email - Use Caution
>
> Dear Freesurfeer experts,
> After running the recon-all in one of my subjets, part of the temporal lobe 
> was partially excluded. Then, I tried to use the watershed algorithm to be 
> less agressive in the skull stripping
> as follows:
>
> recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001
>
> The problem was solved in the brainmask.mgz but not in the cortical surfaces. 
> To
> handle this issue, I edited the white matter and run the recon-all 
> -autorecon2-wm
> -autorecon3 without success. I also placed control points but the following 
> error appeared after running
> the recon-all -autorecon2-cp -autorecon3:
>
> recon-all -s sub_001 existed with errors
>
> I noted that white matter of this part of the temporal lobe has high values 
> (up to 132). What can I
> do to solve the problem with this subject?
>
> Thank you in advance.
>
> Best regards,
> Marina
>
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Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

I'm guessing that the fragments might cause problems later either in gtmseg as 
a hard failure or in gtmpvc as an ill-conditioned matrix. But you can try it 
out:)

On 1/11/2020 6:04 PM, Boris Rauchmann wrote:

External Email - Use Caution

Thanks, that solution seems to work finally. I just ignored the remaining 
voxels labeled according to the standard aseg scheme and proceeded with the the 
PET analysis and the combined LUT.
I will ignore the remaining fragment labels from the original aseg and only use 
the output from the BN labels (starting with 211), these are the only results 
im really interested in. Is that ok?

Here an example stats file I got:

  12 Left-Cerebral-White-Matter  wm 41550 13909.534
0.989   0.0935
  27 Left-Cerebellum-White-Matterwm  2276 1037.525
0.854   0.0811
  38 Left-Cerebellum-Cortex  cortex 10936 6010.637
1.015   0.1339
  4   10 Left-Thalamus-Propersubcort_gm 30.024   
-0.815   0.2251
  5   11 Left-Caudatesubcort_gm 30.035   
21.480   0.1746
  6   12 Left-Putamensubcort_gm250.459
3.161   0.0615
  7   13 Left-Pallidum   subcort_gm491.497
1.474   0.0667
  8   16 Brain-Stem  subcort_gm  4599 2714.856
0.929   0.1000
  9   17 Left-Hippocampussubcort_gm 20.023   
-3.152   0.1702
 10   18 Left-Amygdala   subcort_gm 10.005   
-7.082   0.1060
 11   24 CSF csf 7468 2623.527
0.251   0.2568
 12   26 Left-Accumbens-area subcort_gm 00.004
0.879  nan
 13   28 Left-VentralDC  subcort_gm   714  205.288
1.358   0.1427
 14   31 Left-choroid-plexus csf  220   18.333
5.945   0.6080
 15   41 Right-Cerebral-White-Matter wm 40645 13911.597
0.987   0.0841
 16   46 Right-Cerebellum-White-Matter   wm  2146  990.941
0.862   0.0826
 17   47 Right-Cerebellum-Cortex cortex 11029 6187.241
0.985   0.1317
 18   49 Right-Thalamus-Proper   subcort_gm110.140
0.032   0.2024
 19   50 Right-Caudate   subcort_gm 10.009   
-2.162   0.0258
 20   51 Right-Putamen   subcort_gm442.020
3.727   0.1893
 21   52 Right-Pallidum  subcort_gm240.316
5.739   0.1814
 22   53 Right-Hippocampus   subcort_gm 30.026   
16.575   0.2951
 23   54 Right-Amygdala  subcort_gm 70.081
4.637   0.0897
 24   58 Right-Accumbens-areasubcort_gm 00.000   
-4.474  nan
 25   60 Right-VentralDC subcort_gm   728  198.051
1.430   0.2142
 26   63 Right-choroid-plexuscsf  136   10.088
6.633   0.5924
 27  211 mAmyg_L subcort_gm   264   48.960
1.126   0.1262
 28  212 mAmyg_R subcort_gm   268   46.429
1.292   0.1920
 29  213 lAmyg_L subcort_gm   1316.503
1.889   0.1003
 30  214 lAmyg_R subcort_gm   181   13.490
1.382   0.1237
 31  215 rHipp_L subcort_gm  1020  260.090
1.166   0.1828
 32  216 rHipp_R subcort_gm   833  241.777
1.149   0.2291
 33  217 cHipp_L subcort_gm   911  288.346
1.578   0.3201
 34  218 cHipp_R subcort_gm  1050  330.445
1.273   0.2312
 35  219 vCa_L   subcort_gm   626  170.254
1.205   0.0829
 36  220 vCa_R   subcort_gm   477   84.269
1.491   0.0933
 37  221 GP_Lsubcort_gm   597  133.161
1.369   0.0977
 38  222 GP_Rsubcort_gm   514   93.978
1.491   0.0811
 39  223 NAC_L   subcort_gm   412   67.647
1.348   0.1591
 40  224 NAC_R   subcort_gm   503   87.917
1.240   0.1258
 41  225 vmPu_L  subcort_gm   465  128.509
1.740   0.0783
 42  226 vmPu_R  subcort_gm   367   83.411
1.588   0.0699
 43  227 dCa_L   subcort_gm   997  255.259
0.821   0.1448
 44  228 dCa_R   subcort_gm  1271  405.156
1.017   0.1380
 45  229 

Re: [Freesurfer] average subject with 5th order icosahedron tesselation

[Marina Fernández]

External Email - Use Caution

That's it! Thank you Doug!

Best wishes,
Marina.
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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Thanks, that solution seems to work finally. I just ignored the remaining 
voxels labeled according to the standard aseg scheme and proceeded with the the 
PET analysis and the combined LUT.
I will ignore the remaining fragment labels from the original aseg and only use 
the output from the BN labels (starting with 211), these are the only results 
im really interested in. Is that ok?

Here an example stats file I got:

  12 Left-Cerebral-White-Matter  wm 41550 13909.534
0.989   0.0935
  27 Left-Cerebellum-White-Matterwm  2276 1037.525
0.854   0.0811
  38 Left-Cerebellum-Cortex  cortex 10936 6010.637
1.015   0.1339
  4   10 Left-Thalamus-Propersubcort_gm 30.024   
-0.815   0.2251
  5   11 Left-Caudatesubcort_gm 30.035   
21.480   0.1746
  6   12 Left-Putamensubcort_gm250.459
3.161   0.0615
  7   13 Left-Pallidum   subcort_gm491.497
1.474   0.0667
  8   16 Brain-Stem  subcort_gm  4599 2714.856
0.929   0.1000
  9   17 Left-Hippocampussubcort_gm 20.023   
-3.152   0.1702
 10   18 Left-Amygdala   subcort_gm 10.005   
-7.082   0.1060
 11   24 CSF csf 7468 2623.527
0.251   0.2568
 12   26 Left-Accumbens-area subcort_gm 00.004
0.879  nan
 13   28 Left-VentralDC  subcort_gm   714  205.288
1.358   0.1427
 14   31 Left-choroid-plexus csf  220   18.333
5.945   0.6080
 15   41 Right-Cerebral-White-Matter wm 40645 13911.597
0.987   0.0841
 16   46 Right-Cerebellum-White-Matter   wm  2146  990.941
0.862   0.0826
 17   47 Right-Cerebellum-Cortex cortex 11029 6187.241
0.985   0.1317
 18   49 Right-Thalamus-Proper   subcort_gm110.140
0.032   0.2024
 19   50 Right-Caudate   subcort_gm 10.009   
-2.162   0.0258
 20   51 Right-Putamen   subcort_gm442.020
3.727   0.1893
 21   52 Right-Pallidum  subcort_gm240.316
5.739   0.1814
 22   53 Right-Hippocampus   subcort_gm 30.026   
16.575   0.2951
 23   54 Right-Amygdala  subcort_gm 70.081
4.637   0.0897
 24   58 Right-Accumbens-areasubcort_gm 00.000   
-4.474  nan
 25   60 Right-VentralDC subcort_gm   728  198.051
1.430   0.2142
 26   63 Right-choroid-plexuscsf  136   10.088
6.633   0.5924
 27  211 mAmyg_L subcort_gm   264   48.960
1.126   0.1262
 28  212 mAmyg_R subcort_gm   268   46.429
1.292   0.1920
 29  213 lAmyg_L subcort_gm   1316.503
1.889   0.1003
 30  214 lAmyg_R subcort_gm   181   13.490
1.382   0.1237
 31  215 rHipp_L subcort_gm  1020  260.090
1.166   0.1828
 32  216 rHipp_R subcort_gm   833  241.777
1.149   0.2291
 33  217 cHipp_L subcort_gm   911  288.346
1.578   0.3201
 34  218 cHipp_R subcort_gm  1050  330.445
1.273   0.2312
 35  219 vCa_L   subcort_gm   626  170.254
1.205   0.0829
 36  220 vCa_R   subcort_gm   477   84.269
1.491   0.0933
 37  221 GP_Lsubcort_gm   597  133.161
1.369   0.0977
 38  222 GP_Rsubcort_gm   514   93.978
1.491   0.0811
 39  223 NAC_L   subcort_gm   412   67.647
1.348   0.1591
 40  224 NAC_R   subcort_gm   503   87.917
1.240   0.1258
 41  225 vmPu_L  subcort_gm   465  128.509
1.740   0.0783
 42  226 vmPu_R  subcort_gm   367   83.411
1.588   0.0699
 43  227 dCa_L   subcort_gm   997  255.259
0.821   0.1448
 44  228 dCa_R   subcort_gm  1271  405.156
1.017   0.1380
 45  229 dlPu_L  subcort_gm   678  122.256
1.356   0.0960
 46  230 dlPu_R  subcort_gm   585  150.878
1.319   0.0942
 47  231 mPFtha_L  

Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

On 1/8/2020 10:17 AM, Boris Rauchmann wrote:

External Email - Use Caution

Ok. i figured it out. The problem was just that you can not specify the file 
type - so .mgz in  BN_Atlas_subcotex.mgz was actually the problem.
Ah, ok. This is actually fixed in our development version.

Now I run in a new issue:
I think at last one problem is that your subcortical seg  
BN_Atlas_subcortex.mgz really only has subcortical segmentations, but it needs 
to have the whole head segmeted, including segments for cortex (something like 
the aseg.mgz). Without that, mri_aparc_aseg completes ok but the actual 
segmentation does not have any cortex which is then needed by gtmseg. The road 
forward is a little tricky. You can try something like this:
mergeseg --src aseg.mgz --merge BN_Atlas_subcortex.mgz --o newseg.mgz
This takes the segments from BN and superimposes them on aseg.mgz. You have to 
make sure that the segmentation numbers don't conflict and you will have to 
have a colortable that includes all of the BN and the original aseg. Finally, 
you will need to resolve any inconsistencies, eg, hippo is defined in aseg.mgz 
and in BN, but they will not overlap perfectly, so there will still be some 
voxels labeled as the original aseg hippo. You will have to reassign these 
voxels to a label in BN (same with other structures). You could do this on the 
output of merge seg, or you could go back and regenerate your gca using 
resolved merged segmentations as input


gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz --ctx-annot 
BN_Atlas.annot --ctab 
'/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt'
Wed Jan  8 17:04:12 CET 2020

setenv SUBJECTS_DIR 
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects
cd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects
/usr/local/freesurfer/bin/gtmseg --head BN_apas+head.mgz --s 1122_test --o 
NEU_BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab 
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt

freesurfer-linux-centos6_x86_64-dev-20180911-69aa645
$Id: gtmseg,v 1.19 2016/03/24 17:32:23 greve Exp $
Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 
09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas BN_apas+head.mgz 
--ctx-annot BN_Atlas.annot --ctab 
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
 --no-subseg-wm --no-keep-cc --no-keep-hypo

$Id: mri_gtmseg.c,v 1.10 2016/08/02 21:07:24 greve Exp $
cwd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects
cmdline mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas 
BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab 
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
 --no-subseg-wm --no-keep-cc --no-keep-hypo
sysname  Linux
hostname linuxrechner2
machine  x86_64
user demenzbild
subject 1122_test
USF 2
OutputUSF 2
apasfile BN_apas+head.mgz
wmannotfile NULL
ctxannotfile BN_Atlas.annot
ctxlhbase 1000
ctxrhbase 2000
SubSegWM   0
KeepHypo   0
KeepCC   0
dmax 5.00
nlist   0
lhmin  1000
lhmax  1900
rhmin  2000
rhmax  2900
mri_gtmseg supposed to be reproducible but seed not set
Starting MRIgtmSeg()
Starting MRIgtmSeg() USF=2
Loading 
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/1122_test/mri/BN_apas+head.mgz
Loading surfaces  t = 2.1510
Loading annotations  t = 4.8510
Not segmenting WM
reading colortable from annotation file...
colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt)
reading colortable from annotation file...
colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt)
 Relabeling any unlateralized hypointenities as lateralized hypointenities
  MRIrelabelHypoHemi(): looping over volume
 nthreads = 1
 Relabeling CC as WM
 Relabeling any hypointensities as WM
  MRIunsegmentWM(): looping over volume
 nthreads = 1
Upsampling segmentation USF = 2 t = 7.3520
  MRIhiresSeg(): filling unknowns with 257
Beginning cortical segmentation using BN_Atlas.annot t = 41.3800
  MRIannot2CorticalSeg(): looping over volume
 nthreads = 1
  MRIannot2CorticalSeg(): found 2347 unknown, filled with 257
Not subsegmenting WM
Found 279 segs in the final list
MRIgtmSeg() done, t = 224.1820
Computing colortable
ERROR: cannot find match for subcortical segid 227
ERROR: mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas 
BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab 
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
 --no-subseg-wm --no-keep-cc --no-keep-hypo
gtmseg exited with errors

Before I run gtmseg I used xcerebralseg --s 1122_test --m 
aparc+BN_Atlas_subcotex.mgz --atlas 
'/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_subcortex.gca'
  --o BN_apas+head.mgz

Any ideas on that?

Best,
Boris

Am Mo., 6. Jan. 2020 um 23:14 Uhr schrieb 

Re: [Freesurfer] average subject with 5th order icosahedron tesselation

[Greve, Douglas N.,Ph.D.]

when you make the average subject, just use --ico 5


On 1/9/2020 11:15 AM, Marina Fernández wrote:

External Email - Use Caution

Dear Freesurfer experts,

Now, I would like to downsample the average subject of a dataset (that is a 7th 
order icosahedron tesselation) to have surfaces with 10242 vertices (5th order 
icosahedron tesselation).

How can I do that?

Thank you in advance.

Best regards,
Marina.



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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Ok. i figured it out. The problem was just that you can not specify the
file type - so .mgz in  BN_Atlas_subcotex.mgz was actually the problem.

Now I run in a new issue:

gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz
--ctx-annot BN_Atlas.annot --ctab
'/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt'

Wed Jan  8 17:04:12 CET 2020

setenv SUBJECTS_DIR
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects
cd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects
/usr/local/freesurfer/bin/gtmseg --head BN_apas+head.mgz --s 1122_test --o
NEU_BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt

freesurfer-linux-centos6_x86_64-dev-20180911-69aa645
$Id: gtmseg,v 1.19 2016/03/24 17:32:23 greve Exp $
Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18
09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas
BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
--no-subseg-wm --no-keep-cc --no-keep-hypo

$Id: mri_gtmseg.c,v 1.10 2016/08/02 21:07:24 greve Exp $
cwd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects
cmdline mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas
BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
--no-subseg-wm --no-keep-cc --no-keep-hypo
sysname  Linux
hostname linuxrechner2
machine  x86_64
user demenzbild
subject 1122_test
USF 2
OutputUSF 2
apasfile BN_apas+head.mgz
wmannotfile NULL
ctxannotfile BN_Atlas.annot
ctxlhbase 1000
ctxrhbase 2000
SubSegWM   0
KeepHypo   0
KeepCC   0
dmax 5.00
nlist   0
lhmin  1000
lhmax  1900
rhmin  2000
rhmax  2900
mri_gtmseg supposed to be reproducible but seed not set
Starting MRIgtmSeg()
Starting MRIgtmSeg() USF=2
Loading
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/1122_test/mri/BN_apas+head.mgz
Loading surfaces  t = 2.1510
Loading annotations  t = 4.8510
Not segmenting WM
reading colortable from annotation file...
colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt)
reading colortable from annotation file...
colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt)
 Relabeling any unlateralized hypointenities as lateralized hypointenities
  MRIrelabelHypoHemi(): looping over volume
 nthreads = 1
 Relabeling CC as WM
 Relabeling any hypointensities as WM
  MRIunsegmentWM(): looping over volume
 nthreads = 1
Upsampling segmentation USF = 2 t = 7.3520
  MRIhiresSeg(): filling unknowns with 257
Beginning cortical segmentation using BN_Atlas.annot t = 41.3800
  MRIannot2CorticalSeg(): looping over volume
 nthreads = 1
  MRIannot2CorticalSeg(): found 2347 unknown, filled with 257
Not subsegmenting WM
Found 279 segs in the final list
MRIgtmSeg() done, t = 224.1820
Computing colortable
ERROR: cannot find match for subcortical segid 227
ERROR: mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas
BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
--no-subseg-wm --no-keep-cc --no-keep-hypo
gtmseg exited with errors

Before I run gtmseg I used xcerebralseg --s 1122_test --m
aparc+BN_Atlas_subcotex.mgz --atlas
'/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_subcortex.gca'
 --o BN_apas+head.mgz

Any ideas on that?

Best,
Boris

Am Mo., 6. Jan. 2020 um 23:14 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> Are you sure you have permission to view that file?
>
> On 1/6/20 5:01 PM, Boris Rauchmann wrote:
> >  External Email - Use Caution
> >
> > I’m sure just double checked it. I don’t know what’s wrong here.
> >
> > Von meinem iPhone gesendet
> >
> >>> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu>:
> >> This is not making any sense to me. Are you sure you are in
> >> $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that
> >> BN_Atlas_subcotex.mgz is in the same folder?
> >>
> >>> On 1/3/20 3:07 PM, Boris Rauchmann wrote:
> >>>
> >>>  External Email - Use Caution
> >>>
> >>> Thank you for testing it. As before I get the same error message.
> >>> Do you know what I´m doing wrong here?
> >>>
> >>> Best,
> >>> Boris
> >>>
> >>> MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg
> >>> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
> >>> SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
> >>> subject 1122
> >>> outvol aparc+BN_Atlas_subcotex.mgz
> >>> useribbon 0
> >>> baseoffset 0
> >>> RipUnknown 0
> >>>
> >>> Reading lh white surface
> >>>   /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
> >>>
> >>> Reading lh pial 

Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

Are you sure you have permission to view that file?

On 1/6/20 5:01 PM, Boris Rauchmann wrote:
>  External Email - Use Caution
>
> I’m sure just double checked it. I don’t know what’s wrong here.
>
> Von meinem iPhone gesendet
>
>>> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. 
>>> :
>> This is not making any sense to me. Are you sure you are in
>> $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that
>> BN_Atlas_subcotex.mgz is in the same folder?
>>
>>> On 1/3/20 3:07 PM, Boris Rauchmann wrote:
>>>
>>>  External Email - Use Caution
>>>
>>> Thank you for testing it. As before I get the same error message.
>>> Do you know what I´m doing wrong here?
>>>
>>> Best,
>>> Boris
>>>
>>> MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg
>>> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
>>> SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
>>> subject 1122
>>> outvol aparc+BN_Atlas_subcotex.mgz
>>> useribbon 0
>>> baseoffset 0
>>> RipUnknown 0
>>>
>>> Reading lh white surface
>>>   /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
>>>
>>> Reading lh pial surface
>>>   /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
>>>
>>> Loading lh annotations from
>>> /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot
>>> reading colortable from annotation file...
>>> colortable with 36 entries read (originally
>>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>>>
>>> Reading rh white surface
>>>   /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
>>>
>>> Reading rh pial surface
>>>   /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
>>>
>>> Loading rh annotations from
>>> /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot
>>> reading colortable from annotation file...
>>> colortable with 36 entries read (originally
>>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>>> Have color table for lh white annotation
>>> Have color table for rh white annotation
>>> Loading ribbon segmentation from
>>> /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
>>>
>>> Building hash of lh white
>>>
>>> Building hash of lh pial
>>>
>>> Building hash of rh white
>>>
>>> Building hash of rh pial
>>> ERROR: cannot find aseg
>>> MacBook-Pro:mri boris$
>>>
>>>
 Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D.
 mailto:dgr...@mgh.harvard.edu>>:
 OK, using the data you sent I was able to get mri_aparc2aseg to run.
 Can you try this command again?
 On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
>  External Email - Use Caution
> My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg
> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
> SUBJECTS_DIR /Users/boris/Desktop/mydir
> subject 1122
> outvol aparc+BN_Atlas_subcotex.mgz
> useribbon 0
> baseoffset 0
> RipUnknown 0
> Reading lh white surface
>   /Users/boris/Desktop/mydir/1122/surf/lh.white
> Reading lh pial surface
>   /Users/boris/Desktop/mydir/1122/surf/lh.pial
> Loading lh annotations from
> /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> Reading rh white surface
>   /Users/boris/Desktop/mydir/1122/surf/rh.white
> Reading rh pial surface
>   /Users/boris/Desktop/mydir/1122/surf/rh.pial
> Loading rh annotations from
> /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> Have color table for lh white annotation
> Have color table for rh white annotation
> Loading ribbon segmentation from
> /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
> Building hash of lh white
> Building hash of lh pial
> Building hash of rh white
> Building hash of rh pial
> ERROR: cannot find aseg
> I get the same result using aseg.mgz
> Thanks,
> Boris
>> Am 12.12.2019 um 17:37 schrieb Bruce Fischl
>> mailto:fis...@nmr.mgh.harvard.edu>>:
>> Hi Boris
>> can you send us the full command line and screen output of the
>> commands that are failing?
>> cheers
>> Bruce
>> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
>>>  External Email - Use Caution
>>> Thanks. unfortunately I get an error message when I use the --aseg
>>> flag for BN_Atlas_subcotex.mgz but
>>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find
>>> aseg
>>> .../fs_all_subjects/xyz/mri/aseg.mgz
>>> The file BN_Atlas_subcotex.mgz was created using:
>>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
>>> 

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

I’m sure just double checked it. I don’t know what’s wrong here. 

Von meinem iPhone gesendet

>> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. 
>> :
> This is not making any sense to me. Are you sure you are in 
> $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that 
> BN_Atlas_subcotex.mgz is in the same folder?
> 
>> On 1/3/20 3:07 PM, Boris Rauchmann wrote:
>> 
>> External Email - Use Caution
>> 
>> Thank you for testing it. As before I get the same error message.
>> Do you know what I´m doing wrong here?
>> 
>> Best,
>> Boris
>> 
>> MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
>> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
>> SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
>> subject 1122
>> outvol aparc+BN_Atlas_subcotex.mgz
>> useribbon 0
>> baseoffset 0
>> RipUnknown 0
>> 
>> Reading lh white surface
>>  /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
>> 
>> Reading lh pial surface
>>  /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
>> 
>> Loading lh annotations from 
>> /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally 
>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>> 
>> Reading rh white surface
>>  /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
>> 
>> Reading rh pial surface
>>  /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
>> 
>> Loading rh annotations from 
>> /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally 
>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>> Have color table for lh white annotation
>> Have color table for rh white annotation
>> Loading ribbon segmentation from 
>> /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
>> 
>> Building hash of lh white
>> 
>> Building hash of lh pial
>> 
>> Building hash of rh white
>> 
>> Building hash of rh pial
>> ERROR: cannot find aseg
>> MacBook-Pro:mri boris$
>> 
>> 
>>> Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D.
>>> mailto:dgr...@mgh.harvard.edu>>:
>>> OK, using the data you sent I was able to get mri_aparc2aseg to run.
>>> Can you try this command again?
>>> On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
 External Email - Use Caution
 My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg
 BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
 SUBJECTS_DIR /Users/boris/Desktop/mydir
 subject 1122
 outvol aparc+BN_Atlas_subcotex.mgz
 useribbon 0
 baseoffset 0
 RipUnknown 0
 Reading lh white surface
  /Users/boris/Desktop/mydir/1122/surf/lh.white
 Reading lh pial surface
  /Users/boris/Desktop/mydir/1122/surf/lh.pial
 Loading lh annotations from
 /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
 reading colortable from annotation file...
 colortable with 36 entries read (originally
 /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
 Reading rh white surface
  /Users/boris/Desktop/mydir/1122/surf/rh.white
 Reading rh pial surface
  /Users/boris/Desktop/mydir/1122/surf/rh.pial
 Loading rh annotations from
 /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
 reading colortable from annotation file...
 colortable with 36 entries read (originally
 /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
 Have color table for lh white annotation
 Have color table for rh white annotation
 Loading ribbon segmentation from
 /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
 Building hash of lh white
 Building hash of lh pial
 Building hash of rh white
 Building hash of rh pial
 ERROR: cannot find aseg
 I get the same result using aseg.mgz
 Thanks,
 Boris
> Am 12.12.2019 um 17:37 schrieb Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>>:
> Hi Boris
> can you send us the full command line and screen output of the
> commands that are failing?
> cheers
> Bruce
> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
>> External Email - Use Caution
>> Thanks. unfortunately I get an error message when I use the --aseg
>> flag for BN_Atlas_subcotex.mgz but
>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find
>> aseg
>> .../fs_all_subjects/xyz/mri/aseg.mgz
>> The file BN_Atlas_subcotex.mgz was created using:
>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
>> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
>> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
>> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
>> Best,
>> Boris
>> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D.
>> 

Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

This is not making any sense to me. Are you sure you are in 
$SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that 
BN_Atlas_subcotex.mgz is in the same folder?

On 1/3/20 3:07 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Thank you for testing it. As before I get the same error message.
> Do you know what I´m doing wrong here?
>
> Best,
> Boris
>
> MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
> SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
> subject 1122
> outvol aparc+BN_Atlas_subcotex.mgz
> useribbon 0
> baseoffset 0
> RipUnknown 0
>
> Reading lh white surface
>  /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
>
> Reading lh pial surface
>  /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
>
> Loading lh annotations from 
> /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally 
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>
> Reading rh white surface
>  /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
>
> Reading rh pial surface
>  /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
>
> Loading rh annotations from 
> /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally 
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> Have color table for lh white annotation
> Have color table for rh white annotation
> Loading ribbon segmentation from 
> /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
> ERROR: cannot find aseg
> MacBook-Pro:mri boris$
>
>
>> Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>>:
>>
>> OK, using the data you sent I was able to get mri_aparc2aseg to run. 
>> Can you try this command again?
>>
>> On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
>>>
>>> External Email - Use Caution
>>>
>>> My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
>>> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
>>> SUBJECTS_DIR /Users/boris/Desktop/mydir
>>> subject 1122
>>> outvol aparc+BN_Atlas_subcotex.mgz
>>> useribbon 0
>>> baseoffset 0
>>> RipUnknown 0
>>>
>>> Reading lh white surface
>>>  /Users/boris/Desktop/mydir/1122/surf/lh.white
>>>
>>> Reading lh pial surface
>>>  /Users/boris/Desktop/mydir/1122/surf/lh.pial
>>>
>>> Loading lh annotations from 
>>> /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
>>> reading colortable from annotation file...
>>> colortable with 36 entries read (originally 
>>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>>>
>>> Reading rh white surface
>>>  /Users/boris/Desktop/mydir/1122/surf/rh.white
>>>
>>> Reading rh pial surface
>>>  /Users/boris/Desktop/mydir/1122/surf/rh.pial
>>>
>>> Loading rh annotations from 
>>> /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
>>> reading colortable from annotation file...
>>> colortable with 36 entries read (originally 
>>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>>> Have color table for lh white annotation
>>> Have color table for rh white annotation
>>> Loading ribbon segmentation from 
>>> /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
>>>
>>> Building hash of lh white
>>>
>>> Building hash of lh pial
>>>
>>> Building hash of rh white
>>>
>>> Building hash of rh pial
>>> ERROR: cannot find aseg
>>>
>>>
>>> I get the same result using aseg.mgz
>>>
>>> Thanks,
>>> Boris
 Am 12.12.2019 um 17:37 schrieb Bruce Fischl 
 mailto:fis...@nmr.mgh.harvard.edu>>:

 Hi Boris

 can you send us the full command line and screen output of the 
 commands that are failing?

 cheers
 Bruce
 On Thu, 12 Dec 2019, Boris Rauchmann wrote:

> External Email - Use Caution
> Thanks. unfortunately I get an error message when I use the --aseg 
> flag for BN_Atlas_subcotex.mgz but
> even, if I'm using the original aseg.mgz I get: ERROR: cannot find 
> aseg
> .../fs_all_subjects/xyz/mri/aseg.mgz
> The file BN_Atlas_subcotex.mgz was created using:
> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
> Best,
> Boris
> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but 
> with your
>  subcortical ROIs added? If so, you can try merging it with 
> the aparc, eg,
>
>  mri_aparc2aseg --s subject 

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Thank you for testing it. As before I get the same error message. 
Do you know what I´m doing wrong here?

Best, 
Boris

MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
subject 1122
outvol aparc+BN_Atlas_subcotex.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white

Reading lh pial surface 
 /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial

Loading lh annotations from 
/Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white

Reading rh pial surface 
 /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial

Loading rh annotations from 
/Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from 
/Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial
ERROR: cannot find aseg
MacBook-Pro:mri boris$


> Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you 
> try this command again?
> 
> On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
>> External Email - Use Caution
>> 
>> My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
>> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
>> SUBJECTS_DIR /Users/boris/Desktop/mydir
>> subject 1122
>> outvol aparc+BN_Atlas_subcotex.mgz
>> useribbon 0
>> baseoffset 0
>> RipUnknown 0
>> 
>> Reading lh white surface 
>>  /Users/boris/Desktop/mydir/1122/surf/lh.white
>> 
>> Reading lh pial surface 
>>  /Users/boris/Desktop/mydir/1122/surf/lh.pial
>> 
>> Loading lh annotations from 
>> /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally 
>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>> 
>> Reading rh white surface 
>>  /Users/boris/Desktop/mydir/1122/surf/rh.white
>> 
>> Reading rh pial surface 
>>  /Users/boris/Desktop/mydir/1122/surf/rh.pial
>> 
>> Loading rh annotations from 
>> /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally 
>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>> Have color table for lh white annotation
>> Have color table for rh white annotation
>> Loading ribbon segmentation from 
>> /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
>> 
>> Building hash of lh white
>> 
>> Building hash of lh pial
>> 
>> Building hash of rh white
>> 
>> Building hash of rh pial
>> ERROR: cannot find aseg
>> 
>> 
>> I get the same result using aseg.mgz 
>> 
>> Thanks,
>> Boris
>>> Am 12.12.2019 um 17:37 schrieb Bruce Fischl >> >:
>>> 
>>> Hi Boris
>>> 
>>> can you send us the full command line and screen output of the commands 
>>> that are failing?
>>> 
>>> cheers
>>> Bruce
>>> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
>>> 
 External Email - Use Caution
 Thanks. unfortunately I get an error message when I use the --aseg flag 
 for BN_Atlas_subcotex.mgz but
 even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
 .../fs_all_subjects/xyz/mri/aseg.mgz
 The file BN_Atlas_subcotex.mgz was created using: 
 mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
 $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
 $SUBJECTS_DIR/BN_Atlas_subcortex.gca
 $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
 Best,
 Boris
 On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. 
 mailto:dgr...@mgh.harvard.edu>> wrote:
  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your
  subcortical ROIs added? If so, you can try merging it with the aparc, 
 eg,
 
  mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o
  aparc+BN_Atlas_subcotex.mgz
 
  Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and 
 then
  run gtmseg as you have done below.
 
  Let me know if that works
  doug
 
  On 12/2/19 1:18 PM, Boris Rauchmann wrote:
  >
  > External Email - Use Caution
  

Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you 
try this command again?

On 12/12/2019 11:57 AM, Boris Rauchmann wrote:

External Email - Use Caution

My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
SUBJECTS_DIR /Users/boris/Desktop/mydir
subject 1122
outvol aparc+BN_Atlas_subcotex.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface
 /Users/boris/Desktop/mydir/1122/surf/lh.white

Reading lh pial surface
 /Users/boris/Desktop/mydir/1122/surf/lh.pial

Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface
 /Users/boris/Desktop/mydir/1122/surf/rh.white

Reading rh pial surface
 /Users/boris/Desktop/mydir/1122/surf/rh.pial

Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial
ERROR: cannot find aseg


I get the same result using aseg.mgz

Thanks,
Boris
Am 12.12.2019 um 17:37 schrieb Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>>:

Hi Boris

can you send us the full command line and screen output of the commands that 
are failing?

cheers
Bruce
On Thu, 12 Dec 2019, Boris Rauchmann wrote:

External Email - Use Caution
Thanks. unfortunately I get an error message when I use the --aseg flag for 
BN_Atlas_subcotex.mgz but
even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
.../fs_all_subjects/xyz/mri/aseg.mgz
The file BN_Atlas_subcotex.mgz was created using:
mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
$SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
Best,
Boris
On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
 What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your
 subcortical ROIs added? If so, you can try merging it with the aparc, eg,

 mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o
 aparc+BN_Atlas_subcotex.mgz

 Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then
 run gtmseg as you have done below.

 Let me know if that works
 doug

 On 12/2/19 1:18 PM, Boris Rauchmann wrote:
 >
 > External Email - Use Caution
 >
 > In this example tried it with only the subcortical segmentations from
 > my atlas. Please find the logfile attached. It gives me back: "tissue
 > type is not set" but I set it to 2 in the LUT.txt
 >
 > In principle look the following commands right to you?
 >
 > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
 > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
 >
 > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
 > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
 >
 > Ideally I would have a gtmseg with both, the subcortical and the
 > cortical structures, but only the subcortical would also be fine as
 > long as I can get  mri_gtmpvc running on it.
 >
 > Thanks,
 > Boris
 >
 > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
 > mailto:dgr...@mgh.harvard.edu> 
> wrote:
 >
 > Can you send the log file for each of the gtmseg runs?
 >
 > On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
 >>
 >> External Email - Use Caution
 >>
 >> Thank you! I have a gca for subcortical  and two gcs (lh/rh) for
 >> cortical structures.
 >> I created an annot (rh/lh) and a mgz using mris_ca_label
 >> and mri_ca_label for parcellation/segmentation stats.
 >>
 >> For the PET analysis I have the following problem:
 >>
 >> If I use this command: gtmseg --s test --o test.mgz --ctab
 >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz
 >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
 >>
 >> It gives me the right regions for subcortical structures but it
 >> looks like it uses the standard FS parcellation with my labels
 >> for the cortical parcellations (only 93 cortical regions instead
 >> of 210).
 >>
 >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz
 >> --ctx-annot BN_Atlas.annot --ctab 

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Dear Douglas,

I uploaded two files: 1122.tar.gz is the sample subject and 
BN_Atlas_freesurfer.tar.gz this is the Atlas I want use for the cortical and 
subcortical parcellation/segmentation.

Thank you so much,
Boris


> Am 02.01.2020 um 17:06 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> .

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

Can you send me the subject data following these steps?

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.



On 12/20/2019 10:58 AM, Boris Rauchmann wrote:

External Email - Use Caution

I had a look at the mgz file with freeview and it actually looks fine to me. 
Its the subcortical segmentation of the BN atlas.
Do you have any ideas what went wrong?

Best,
Boris

On Tue, Dec 17, 2019 at 6:33 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
OK, I'm still at a loss. The one suspicious thing is that it only took a few 
min to run. So you have never looked at that volume? What is in the atlas?

On 12/16/2019 3:42 PM, Boris Rauchmann wrote:

External Email - Use Caution

This is the log when I´m creating this file:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label 
$SUBJECTS_DIR/1122/mri/brain.mgz 
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z 
$SUBJECTS_DIR/BN_Atlas_subcortex.gca 
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
sysname  Darwin
hostname MacBook.local
machine  x86_64

setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer
mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz 
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca 
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz


== Number of threads available to mri_ca_label for OpenMP = 1 ==
reading 1 input volumes
reading classifier array from 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
reading input volume from /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
reading transform from 
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 4.97
Atlas used for the 3D morph was 
/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 10.8   using min determinant for regularization = 11.7
0 singular and 129 ill-conditioned covariance matrices regularized
labeling volume...
0 gm and wm labels changed (%nan to gray, %nan to white out of all changed 
labels)
0 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 9576 changed.
pass 2: 3286 changed.
MRItoUCHAR: min=0, max=246
MRItoUCHAR: converting to UCHAR
writing labeled volume to 
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
mri_ca_label utimesec146.184667
mri_ca_label stimesec1.040963
mri_ca_label ru_maxrss   1436573696
mri_ca_label ru_ixrss0
mri_ca_label ru_idrss0
mri_ca_label ru_isrss0
mri_ca_label ru_minflt   609288
mri_ca_label ru_majflt   112
mri_ca_label ru_nswap0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  4
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw3
mri_ca_label ru_nivcsw   36417
auto-labeling took 2 minutes and 28 seconds.

This is what I get when I do mrs_info on the gas:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_info 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca
reading frame -1 of gca
Volume information for 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca
  type: GCA
dimensions: 256 x 256 x 256 x 3
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 3
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 0.
  : x_a =   0., y_a =   0., z_a =   1., c_a = 0.
  : x_s =   0., y_s =  -1., z_s =   0., c_s = 0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0.   128.
0.   0.   1.  -128.
0.  -1.   0.   128.
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   128.
   -0.  -0.  -1.   128.
   -0.   1.  -0.   128.
   -0.  -0.  -0. 1.




Am 16.12.2019 um 21:21 schrieb Boris Rauchmann 
mailto:boris.rauchm...@gmail.com>>:

Thanks, it was created using:

mri_ca_label 

Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

OK, I'm still at a loss. The one suspicious thing is that it only took a few 
min to run. So you have never looked at that volume? What is in the atlas?

On 12/16/2019 3:42 PM, Boris Rauchmann wrote:

External Email - Use Caution

This is the log when I´m creating this file:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label 
$SUBJECTS_DIR/1122/mri/brain.mgz 
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z 
$SUBJECTS_DIR/BN_Atlas_subcortex.gca 
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
sysname  Darwin
hostname MacBook.local
machine  x86_64

setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer
mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz 
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca 
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz


== Number of threads available to mri_ca_label for OpenMP = 1 ==
reading 1 input volumes
reading classifier array from 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
reading input volume from /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
reading transform from 
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 4.97
Atlas used for the 3D morph was 
/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 10.8   using min determinant for regularization = 11.7
0 singular and 129 ill-conditioned covariance matrices regularized
labeling volume...
0 gm and wm labels changed (%nan to gray, %nan to white out of all changed 
labels)
0 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 9576 changed.
pass 2: 3286 changed.
MRItoUCHAR: min=0, max=246
MRItoUCHAR: converting to UCHAR
writing labeled volume to 
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
mri_ca_label utimesec146.184667
mri_ca_label stimesec1.040963
mri_ca_label ru_maxrss   1436573696
mri_ca_label ru_ixrss0
mri_ca_label ru_idrss0
mri_ca_label ru_isrss0
mri_ca_label ru_minflt   609288
mri_ca_label ru_majflt   112
mri_ca_label ru_nswap0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  4
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw3
mri_ca_label ru_nivcsw   36417
auto-labeling took 2 minutes and 28 seconds.

This is what I get when I do mrs_info on the gas:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_info 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca
reading frame -1 of gca
Volume information for 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca
  type: GCA
dimensions: 256 x 256 x 256 x 3
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 3
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 0.
  : x_a =   0., y_a =   0., z_a =   1., c_a = 0.
  : x_s =   0., y_s =  -1., z_s =   0., c_s = 0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0.   128.
0.   0.   1.  -128.
0.  -1.   0.   128.
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   128.
   -0.  -0.  -1.   128.
   -0.   1.  -0.   128.
   -0.  -0.  -0. 1.




Am 16.12.2019 um 21:21 schrieb Boris Rauchmann 
mailto:boris.rauchm...@gmail.com>>:

Thanks, it was created using:

mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz

Best,
Boris


Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>>:

There is something weird about that file. How was it created?
doug
ps. Please include previous correspondence in the email

On 12/16/19 1:12 PM, Boris Rauchmann wrote:

External Email - Use Caution

Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz,
-1): could not open file

Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu> 
>:

mri_info N_Atlas_subcotex.mgz


___
Freesurfer mailing list

Re: [Freesurfer] (no subject)

[Bruce Fischl]

sorry, my fault. That was for someone else
On Mon, 16 Dec 2019, Boris 
Rauchmann wrote:




External Email - Use Caution

This is the log when I´m creating this file:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label
$SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
sysname  Darwin
hostname MacBook.local
machine  x86_64

setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer
mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz 


== Number of threads available to mri_ca_label for OpenMP = 1 == 
reading 1 input volumes
reading classifier array from
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
reading input volume from
/Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
reading transform from
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 4.97
Atlas used for the 3D morph was
/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 10.8   using min determinant for regularization = 11.7
0 singular and 129 ill-conditioned covariance matrices regularized
labeling volume...
0 gm and wm labels changed (%nan to gray, %nan to white out of all changed
labels)
0 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 9576 changed.
pass 2: 3286 changed.
MRItoUCHAR: min=0, max=246
MRItoUCHAR: converting to UCHAR
writing labeled volume to
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
mri_ca_label utimesec    146.184667
mri_ca_label stimesec    1.040963
mri_ca_label ru_maxrss   1436573696
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   609288
mri_ca_label ru_majflt   112
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  4
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    3
mri_ca_label ru_nivcsw   36417
auto-labeling took 2 minutes and 28 seconds.

This is what I get when I do mrs_info on the gas:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ 
mri_info/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gc
a 
reading frame -1 of gca
Volume information 
for/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gc
a
          type: GCA
    dimensions: 256 x 256 x 256 x 3
   voxel sizes: 1.00, 1.00, 1.00
          type: FLOAT (3)
           fov: 256.000
           dof: 0
        xstart: -128.0, xend: 128.0
        ystart: -128.0, yend: 128.0
        zstart: -128.0, zend: 128.0
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
       nframes: 3
       PhEncDir: UNKNOWN
       FieldStrength: 0.00
ras xform present
    xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =    
0.
              : x_a =   0., y_a =   0., z_a =   1., c_a =    
0.
              : x_s =   0., y_s =  -1., z_s =   0., c_s =    
0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.   0.   0.   128.
                0.   0.   1.  -128.
                0.  -1.   0.   128.
                0.   0.   0.     1.

voxel-to-ras determinant -1

ras to voxel transform:
               -1.  -0.  -0.   128.
               -0.  -0.  -1.   128.
               -0.   1.  -0.   128.
               -0.  -0.  -0.     1.




  Am 16.12.2019 um 21:21 schrieb Boris Rauchmann
  :

Thanks, it was created using: 
mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz

Best,
Boris


  Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D.
  :

There is something weird about that file. How was it created?
doug
ps. Please include previous correspondence in the email

On 12/16/19 1:12 PM, Boris Rauchmann wrote:

  External Email - Use Caution

  Boriss-MacBook-Pro:mri boris$ mri_info
  N_Atlas_subcotex.mgz
  mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz,
  -1): could not open file

Am 16.12.2019 um 19:08 schrieb Greve,
Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>>:

mri_info N_Atlas_subcotex.mgz



  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] (no subject)

[Bruce Fischl]

to summarize, I want a warp that:

foreach subject

   compute warp based on curvature
   apply warp to a functional overlay
   add that functional overlay to avg

return (tf.reduce_mean(tf.square(avg)))


make sense? So maximizing the mean squared average acivation

On Mon, 16 Dec 2019, Boris Rauchmann 
wrote:




External Email - Use Caution

This is the log when I´m creating this file:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label
$SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
sysname  Darwin
hostname MacBook.local
machine  x86_64

setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer
mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz 


== Number of threads available to mri_ca_label for OpenMP = 1 == 
reading 1 input volumes
reading classifier array from
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
reading input volume from
/Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
reading transform from
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 4.97
Atlas used for the 3D morph was
/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 10.8   using min determinant for regularization = 11.7
0 singular and 129 ill-conditioned covariance matrices regularized
labeling volume...
0 gm and wm labels changed (%nan to gray, %nan to white out of all changed
labels)
0 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 9576 changed.
pass 2: 3286 changed.
MRItoUCHAR: min=0, max=246
MRItoUCHAR: converting to UCHAR
writing labeled volume to
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
mri_ca_label utimesec    146.184667
mri_ca_label stimesec    1.040963
mri_ca_label ru_maxrss   1436573696
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   609288
mri_ca_label ru_majflt   112
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  4
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    3
mri_ca_label ru_nivcsw   36417
auto-labeling took 2 minutes and 28 seconds.

This is what I get when I do mrs_info on the gas:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ 
mri_info/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gc
a 
reading frame -1 of gca
Volume information 
for/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gc
a
          type: GCA
    dimensions: 256 x 256 x 256 x 3
   voxel sizes: 1.00, 1.00, 1.00
          type: FLOAT (3)
           fov: 256.000
           dof: 0
        xstart: -128.0, xend: 128.0
        ystart: -128.0, yend: 128.0
        zstart: -128.0, zend: 128.0
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
       nframes: 3
       PhEncDir: UNKNOWN
       FieldStrength: 0.00
ras xform present
    xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =    
0.
              : x_a =   0., y_a =   0., z_a =   1., c_a =    
0.
              : x_s =   0., y_s =  -1., z_s =   0., c_s =    
0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.   0.   0.   128.
                0.   0.   1.  -128.
                0.  -1.   0.   128.
                0.   0.   0.     1.

voxel-to-ras determinant -1

ras to voxel transform:
               -1.  -0.  -0.   128.
               -0.  -0.  -1.   128.
               -0.   1.  -0.   128.
               -0.  -0.  -0.     1.




  Am 16.12.2019 um 21:21 schrieb Boris Rauchmann
  :

Thanks, it was created using: 
mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz

Best,
Boris


  Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D.
  :

There is something weird about that file. How was it created?
doug
ps. Please include previous correspondence in the email

On 12/16/19 1:12 PM, Boris Rauchmann wrote:

  External Email - Use Caution

  Boriss-MacBook-Pro:mri boris$ mri_info
  N_Atlas_subcotex.mgz
  mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz,
  -1): could not open file

Am 16.12.2019 um 19:08 schrieb Greve,
Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>>:

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

This is the log when I´m creating this file:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label 
$SUBJECTS_DIR/1122/mri/brain.mgz 
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z 
$SUBJECTS_DIR/BN_Atlas_subcortex.gca 
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
sysname  Darwin
hostname MacBook.local
machine  x86_64

setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer
mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz 
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca 
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz 


== Number of threads available to mri_ca_label for OpenMP = 1 == 
reading 1 input volumes
reading classifier array from 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
reading input volume from /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
reading transform from 
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 4.97
Atlas used for the 3D morph was 
/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 10.8   using min determinant for regularization = 11.7
0 singular and 129 ill-conditioned covariance matrices regularized
labeling volume...
0 gm and wm labels changed (%nan to gray, %nan to white out of all changed 
labels)
0 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 9576 changed.
pass 2: 3286 changed.
MRItoUCHAR: min=0, max=246
MRItoUCHAR: converting to UCHAR
writing labeled volume to 
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
mri_ca_label utimesec146.184667
mri_ca_label stimesec1.040963
mri_ca_label ru_maxrss   1436573696
mri_ca_label ru_ixrss0
mri_ca_label ru_idrss0
mri_ca_label ru_isrss0
mri_ca_label ru_minflt   609288
mri_ca_label ru_majflt   112
mri_ca_label ru_nswap0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  4
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw3
mri_ca_label ru_nivcsw   36417
auto-labeling took 2 minutes and 28 seconds.

This is what I get when I do mrs_info on the gas:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_info 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca 
reading frame -1 of gca
Volume information for 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca
  type: GCA
dimensions: 256 x 256 x 256 x 3
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 3
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 0.
  : x_a =   0., y_a =   0., z_a =   1., c_a = 0.
  : x_s =   0., y_s =  -1., z_s =   0., c_s = 0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0.   128.
0.   0.   1.  -128.
0.  -1.   0.   128.
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   128.
   -0.  -0.  -1.   128.
   -0.   1.  -0.   128.
   -0.  -0.  -0. 1.




> Am 16.12.2019 um 21:21 schrieb Boris Rauchmann :
> 
> Thanks, it was created using: 
> 
> mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
> $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
> $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
> 
> Best,
> Boris
> 
> 
>> Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>>:
>> 
>> There is something weird about that file. How was it created?
>> doug
>> ps. Please include previous correspondence in the email
>> 
>> On 12/16/19 1:12 PM, Boris Rauchmann wrote:
>>> 
>>> External Email - Use Caution
>>> 
>>> Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
>>> mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, 
>>> -1): could not open file
>>> 
 Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. 
 mailto:dgr...@mgh.harvard.edu> 
 >>:
 
 mri_info N_Atlas_subcotex.mgz
>>> 
>>> 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu 
>>> 

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Thanks, it was created using: 

mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz

Best,
Boris


> Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> There is something weird about that file. How was it created?
> doug
> ps. Please include previous correspondence in the email
> 
> On 12/16/19 1:12 PM, Boris Rauchmann wrote:
>> 
>> External Email - Use Caution
>> 
>> Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
>> mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, 
>> -1): could not open file
>> 
>>> Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. 
>>> mailto:dgr...@mgh.harvard.edu>>:
>>> 
>>> mri_info N_Atlas_subcotex.mgz
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
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Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

There is something weird about that file. How was it created?
doug
ps. Please include previous correspondence in the email

On 12/16/19 1:12 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
> mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, 
> -1): could not open file
>
>> Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>>:
>>
>> mri_info N_Atlas_subcotex.mgz
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1): 
could not open file

> Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> mri_info N_Atlas_subcotex.mgz

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Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

OK, now I'm really confused. Try this
mri_info N_Atlas_subcotex.mgz


On 12/14/19 3:04 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Here the results:
>
>
> pwd:
> /Users/boris/Desktop/MirLIND_test/1122/mri
>
> ls -l BN_Atlas_subcotex.mgz:
> -rwxrwxrwx 1 boris  staff  37013 13 Aug 23:30 BN_Atlas_subcotex.mgz
>
> Best,
> Boris
>> Am 13.12.2019 um 23:53 schrieb Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>>:
>>
>> pwd
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Here the results:


pwd:
/Users/boris/Desktop/MirLIND_test/1122/mri

ls -l BN_Atlas_subcotex.mgz:
-rwxrwxrwx  1 boris  staff  37013 13 Aug 23:30 BN_Atlas_subcotex.mgz

Best,
Boris
> Am 13.12.2019 um 23:53 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> pwd

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Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

ok, this is very strange to me. Can you send the result of these two commands
  pwd
and
  ls -l BN_Atlas_subcotex.mgz


On 12/13/2019 2:22 AM, Boris Rauchmann wrote:

External Email - Use Caution

yes to both. I always get the error ERROR: cannot find aseg...

On Fri, Dec 13, 2019 at 12:58 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that
folder?

On 12/12/19 12:57 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg
> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
> SUBJECTS_DIR /Users/boris/Desktop/mydir
> subject 1122
> outvol aparc+BN_Atlas_subcotex.mgz
> useribbon 0
> baseoffset 0
> RipUnknown 0
>
> Reading lh white surface
>  /Users/boris/Desktop/mydir/1122/surf/lh.white
>
> Reading lh pial surface
>  /Users/boris/Desktop/mydir/1122/surf/lh.pial
>
> Loading lh annotations from
> /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>
> Reading rh white surface
>  /Users/boris/Desktop/mydir/1122/surf/rh.white
>
> Reading rh pial surface
>  /Users/boris/Desktop/mydir/1122/surf/rh.pial
>
> Loading rh annotations from
> /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> Have color table for lh white annotation
> Have color table for rh white annotation
> Loading ribbon segmentation from
> /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
> ERROR: cannot find aseg
>
>
> I get the same result using aseg.mgz
>
> Thanks,
> Boris
>> Am 12.12.2019 um 17:37 schrieb Bruce Fischl
>> mailto:fis...@nmr.mgh.harvard.edu> 
>> >>:
>>
>> Hi Boris
>>
>> can you send us the full command line and screen output of the
>> commands that are failing?
>>
>> cheers
>> Bruce
>> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
>>
>>> External Email - Use Caution
>>> Thanks. unfortunately I get an error message when I use the --aseg
>>> flag for BN_Atlas_subcotex.mgz but
>>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
>>> .../fs_all_subjects/xyz/mri/aseg.mgz
>>> The file BN_Atlas_subcotex.mgz was created using:
>>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
>>> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
>>> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
>>> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
>>> Best,
>>> Boris
>>> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D.
>>> mailto:dgr...@mgh.harvard.edu> 
>>> >> wrote:
>>>  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with
>>> your
>>>  subcortical ROIs added? If so, you can try merging it with the
>>> aparc, eg,
>>>
>>>  mri_aparc2aseg --s subject --volmask --aseg
>>> BN_Atlas_subcotex.mgz --o
>>>  aparc+BN_Atlas_subcotex.mgz
>>>
>>>  Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg,
>>> and then
>>>  run gtmseg as you have done below.
>>>
>>>  Let me know if that works
>>>  doug
>>>
>>>  On 12/2/19 1:18 PM, Boris Rauchmann wrote:
>>>  >
>>>  > External Email - Use Caution
>>>  >
>>>  > In this example tried it with only the subcortical
>>> segmentations from
>>>  > my atlas. Please find the logfile attached. It gives me back:
>>> "tissue
>>>  > type is not set" but I set it to 2 in the LUT.txt
>>>  >
>>>  > In principle look the following commands right to you?
>>>  >
>>>  > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
>>>  > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
>>>  >
>>>  > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
>>>  > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
>>>  >
>>>  > Ideally I would have a gtmseg with both, the subcortical and the
>>>  > cortical structures, but only the subcortical would also be
>>> fine as
>>>  > long as I can get  mri_gtmpvc running on it.
>>>  >
>>>  > Thanks,
>>>  > Boris
>>>  >
>>>  > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
>>>  > mailto:dgr...@mgh.harvard.edu> 
>>> >
>>> >> wrote:
>>>  >
>>>  > Can you send the log file for each of the gtmseg runs?
>>>  >
>>>  > On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
>>>  >>
>>>  >> External 

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

yes to both. I always get the error ERROR: cannot find aseg...

On Fri, Dec 13, 2019 at 12:58 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that
> folder?
>
> On 12/12/19 12:57 PM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg
> > BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
> > SUBJECTS_DIR /Users/boris/Desktop/mydir
> > subject 1122
> > outvol aparc+BN_Atlas_subcotex.mgz
> > useribbon 0
> > baseoffset 0
> > RipUnknown 0
> >
> > Reading lh white surface
> >  /Users/boris/Desktop/mydir/1122/surf/lh.white
> >
> > Reading lh pial surface
> >  /Users/boris/Desktop/mydir/1122/surf/lh.pial
> >
> > Loading lh annotations from
> > /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
> > reading colortable from annotation file...
> > colortable with 36 entries read (originally
> >
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> >
> > Reading rh white surface
> >  /Users/boris/Desktop/mydir/1122/surf/rh.white
> >
> > Reading rh pial surface
> >  /Users/boris/Desktop/mydir/1122/surf/rh.pial
> >
> > Loading rh annotations from
> > /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
> > reading colortable from annotation file...
> > colortable with 36 entries read (originally
> >
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> > Have color table for lh white annotation
> > Have color table for rh white annotation
> > Loading ribbon segmentation from
> > /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
> >
> > Building hash of lh white
> >
> > Building hash of lh pial
> >
> > Building hash of rh white
> >
> > Building hash of rh pial
> > ERROR: cannot find aseg
> >
> >
> > I get the same result using aseg.mgz
> >
> > Thanks,
> > Boris
> >> Am 12.12.2019 um 17:37 schrieb Bruce Fischl
> >> mailto:fis...@nmr.mgh.harvard.edu>>:
> >>
> >> Hi Boris
> >>
> >> can you send us the full command line and screen output of the
> >> commands that are failing?
> >>
> >> cheers
> >> Bruce
> >> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
> >>
> >>> External Email - Use Caution
> >>> Thanks. unfortunately I get an error message when I use the --aseg
> >>> flag for BN_Atlas_subcotex.mgz but
> >>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
> >>> .../fs_all_subjects/xyz/mri/aseg.mgz
> >>> The file BN_Atlas_subcotex.mgz was created using:
> >>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
> >>> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
> >>> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
> >>> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
> >>> Best,
> >>> Boris
> >>> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D.
> >>> mailto:dgr...@mgh.harvard.edu>> wrote:
> >>>  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with
> >>> your
> >>>  subcortical ROIs added? If so, you can try merging it with the
> >>> aparc, eg,
> >>>
> >>>  mri_aparc2aseg --s subject --volmask --aseg
> >>> BN_Atlas_subcotex.mgz --o
> >>>  aparc+BN_Atlas_subcotex.mgz
> >>>
> >>>  Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg,
> >>> and then
> >>>  run gtmseg as you have done below.
> >>>
> >>>  Let me know if that works
> >>>  doug
> >>>
> >>>  On 12/2/19 1:18 PM, Boris Rauchmann wrote:
> >>>  >
> >>>  > External Email - Use Caution
> >>>  >
> >>>  > In this example tried it with only the subcortical
> >>> segmentations from
> >>>  > my atlas. Please find the logfile attached. It gives me back:
> >>> "tissue
> >>>  > type is not set" but I set it to 2 in the LUT.txt
> >>>  >
> >>>  > In principle look the following commands right to you?
> >>>  >
> >>>  > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
> >>>  > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
> >>>  >
> >>>  > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
> >>>  > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
> >>>  >
> >>>  > Ideally I would have a gtmseg with both, the subcortical and the
> >>>  > cortical structures, but only the subcortical would also be
> >>> fine as
> >>>  > long as I can get  mri_gtmpvc running on it.
> >>>  >
> >>>  > Thanks,
> >>>  > Boris
> >>>  >
> >>>  > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
> >>>  > mailto:dgr...@mgh.harvard.edu>
> >>> > wrote:
> >>>  >
> >>>  > Can you send the log file for each of the gtmseg runs?
> >>>  >
> >>>  > On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
> >>>  >>
> >>>  >> External Email - Use Caution
> >>>  >>
> >>>  >> Thank you! I have a gca for subcortical  and two gcs
> >>> (lh/rh) for
> >>>  >>  

Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that 
folder?

On 12/12/19 12:57 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
> SUBJECTS_DIR /Users/boris/Desktop/mydir
> subject 1122
> outvol aparc+BN_Atlas_subcotex.mgz
> useribbon 0
> baseoffset 0
> RipUnknown 0
>
> Reading lh white surface
>  /Users/boris/Desktop/mydir/1122/surf/lh.white
>
> Reading lh pial surface
>  /Users/boris/Desktop/mydir/1122/surf/lh.pial
>
> Loading lh annotations from 
> /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally 
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>
> Reading rh white surface
>  /Users/boris/Desktop/mydir/1122/surf/rh.white
>
> Reading rh pial surface
>  /Users/boris/Desktop/mydir/1122/surf/rh.pial
>
> Loading rh annotations from 
> /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally 
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> Have color table for lh white annotation
> Have color table for rh white annotation
> Loading ribbon segmentation from 
> /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
> ERROR: cannot find aseg
>
>
> I get the same result using aseg.mgz
>
> Thanks,
> Boris
>> Am 12.12.2019 um 17:37 schrieb Bruce Fischl 
>> mailto:fis...@nmr.mgh.harvard.edu>>:
>>
>> Hi Boris
>>
>> can you send us the full command line and screen output of the 
>> commands that are failing?
>>
>> cheers
>> Bruce
>> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
>>
>>> External Email - Use Caution
>>> Thanks. unfortunately I get an error message when I use the --aseg 
>>> flag for BN_Atlas_subcotex.mgz but
>>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
>>> .../fs_all_subjects/xyz/mri/aseg.mgz
>>> The file BN_Atlas_subcotex.mgz was created using:
>>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
>>> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
>>> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
>>> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
>>> Best,
>>> Boris
>>> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. 
>>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>>  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with 
>>> your
>>>  subcortical ROIs added? If so, you can try merging it with the 
>>> aparc, eg,
>>>
>>>  mri_aparc2aseg --s subject --volmask --aseg 
>>> BN_Atlas_subcotex.mgz --o
>>>  aparc+BN_Atlas_subcotex.mgz
>>>
>>>  Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, 
>>> and then
>>>  run gtmseg as you have done below.
>>>
>>>  Let me know if that works
>>>  doug
>>>
>>>  On 12/2/19 1:18 PM, Boris Rauchmann wrote:
>>>  >
>>>  > External Email - Use Caution
>>>  >
>>>  > In this example tried it with only the subcortical 
>>> segmentations from
>>>  > my atlas. Please find the logfile attached. It gives me back: 
>>> "tissue
>>>  > type is not set" but I set it to 2 in the LUT.txt
>>>  >
>>>  > In principle look the following commands right to you?
>>>  >
>>>  > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
>>>  > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
>>>  >
>>>  > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
>>>  > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
>>>  >
>>>  > Ideally I would have a gtmseg with both, the subcortical and the
>>>  > cortical structures, but only the subcortical would also be 
>>> fine as
>>>  > long as I can get  mri_gtmpvc running on it.
>>>  >
>>>  > Thanks,
>>>  > Boris
>>>  >
>>>  > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
>>>  > mailto:dgr...@mgh.harvard.edu> 
>>> > wrote:
>>>  >
>>>  >     Can you send the log file for each of the gtmseg runs?
>>>  >
>>>  >     On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
>>>  >>
>>>  >>     External Email - Use Caution
>>>  >>
>>>  >>     Thank you! I have a gca for subcortical  and two gcs 
>>> (lh/rh) for
>>>  >>     cortical structures.
>>>  >>     I created an annot (rh/lh) and a mgz using mris_ca_label
>>>  >>     and mri_ca_label for parcellation/segmentation stats.
>>>  >>
>>>  >>     For the PET analysis I have the following problem:
>>>  >>
>>>  >>     If I use this command: gtmseg --s test --o test.mgz --ctab
>>>  >>     /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz
>>>  >>     --ctx-annot BN_Atlas.annot --ctab 
>>> 

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
SUBJECTS_DIR /Users/boris/Desktop/mydir
subject 1122
outvol aparc+BN_Atlas_subcotex.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /Users/boris/Desktop/mydir/1122/surf/lh.white

Reading lh pial surface 
 /Users/boris/Desktop/mydir/1122/surf/lh.pial

Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /Users/boris/Desktop/mydir/1122/surf/rh.white

Reading rh pial surface 
 /Users/boris/Desktop/mydir/1122/surf/rh.pial

Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial
ERROR: cannot find aseg


I get the same result using aseg.mgz 

Thanks,
Boris
> Am 12.12.2019 um 17:37 schrieb Bruce Fischl :
> 
> Hi Boris
> 
> can you send us the full command line and screen output of the commands that 
> are failing?
> 
> cheers
> Bruce
> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
> 
>> External Email - Use Caution
>> Thanks. unfortunately I get an error message when I use the --aseg flag for 
>> BN_Atlas_subcotex.mgz but
>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
>> .../fs_all_subjects/xyz/mri/aseg.mgz
>> The file BN_Atlas_subcotex.mgz was created using: 
>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
>> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
>> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
>> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
>> Best,
>> Boris
>> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. 
>>  wrote:
>>  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your
>>  subcortical ROIs added? If so, you can try merging it with the aparc, 
>> eg,
>> 
>>  mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o
>>  aparc+BN_Atlas_subcotex.mgz
>> 
>>  Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then
>>  run gtmseg as you have done below.
>> 
>>  Let me know if that works
>>  doug
>> 
>>  On 12/2/19 1:18 PM, Boris Rauchmann wrote:
>>  >
>>  > External Email - Use Caution
>>  >
>>  > In this example tried it with only the subcortical segmentations from
>>  > my atlas. Please find the logfile attached. It gives me back: "tissue
>>  > type is not set" but I set it to 2 in the LUT.txt
>>  >
>>  > In principle look the following commands right to you?
>>  >
>>  > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
>>  > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
>>  >
>>  > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
>>  > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
>>  >
>>  > Ideally I would have a gtmseg with both, the subcortical and the
>>  > cortical structures, but only the subcortical would also be fine as
>>  > long as I can get  mri_gtmpvc running on it.
>>  >
>>  > Thanks,
>>  > Boris
>>  >
>>  > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
>>  > mailto:dgr...@mgh.harvard.edu>> wrote:
>>  >
>>  > Can you send the log file for each of the gtmseg runs?
>>  >
>>  > On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
>>  >>
>>  >> External Email - Use Caution
>>  >>
>>  >> Thank you! I have a gca for subcortical  and two gcs (lh/rh) for
>>  >> cortical structures.
>>  >> I created an annot (rh/lh) and a mgz using mris_ca_label
>>  >> and mri_ca_label for parcellation/segmentation stats.
>>  >>
>>  >> For the PET analysis I have the following problem:
>>  >>
>>  >> If I use this command: gtmseg --s test --o test.mgz --ctab
>>  >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz
>>  >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
>>  >>
>>  >> It gives me the right regions for subcortical structures but it
>>  >> looks like it uses the standard FS parcellation with my labels
>>  >> for the cortical parcellations (only 93 cortical regions instead
>>  >> of 210).
>>  >>
>>  >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz
>>  >> --ctx-annot 

Re: [Freesurfer] (no subject)

[Bruce Fischl]

Hi Boris

can you send us the full command line and screen output of the commands 
that are failing?


cheers
Bruce
On Thu, 12 Dec 
2019, Boris Rauchmann wrote:




External Email - Use Caution

Thanks. unfortunately I get an error message when I use the --aseg flag for 
BN_Atlas_subcotex.mgz but
even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
.../fs_all_subjects/xyz/mri/aseg.mgz

The file BN_Atlas_subcotex.mgz was created using: 
mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
$SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
Best,
Boris

On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. 
 wrote:
  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your
  subcortical ROIs added? If so, you can try merging it with the aparc, eg,

  mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o
  aparc+BN_Atlas_subcotex.mgz

  Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then
  run gtmseg as you have done below.

  Let me know if that works
  doug


  On 12/2/19 1:18 PM, Boris Rauchmann wrote:
  >
  > External Email - Use Caution
  >
  > In this example tried it with only the subcortical segmentations from
  > my atlas. Please find the logfile attached. It gives me back: "tissue
  > type is not set" but I set it to 2 in the LUT.txt
  >
  > In principle look the following commands right to you?
  >
  > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
  > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
  >
  > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
  > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
  >
  > Ideally I would have a gtmseg with both, the subcortical and the
  > cortical structures, but only the subcortical would also be fine as
  > long as I can get  mri_gtmpvc running on it.
  >
  > Thanks,
  > Boris
  >
  > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
  > mailto:dgr...@mgh.harvard.edu>> wrote:
  >
  >     Can you send the log file for each of the gtmseg runs?
  >
  >     On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
  >>
  >>     External Email - Use Caution
  >>
  >>     Thank you! I have a gca for subcortical  and two gcs (lh/rh) for
  >>     cortical structures.
  >>     I created an annot (rh/lh) and a mgz using mris_ca_label
  >>     and mri_ca_label for parcellation/segmentation stats.
  >>
  >>     For the PET analysis I have the following problem:
  >>
  >>     If I use this command: gtmseg --s test --o test.mgz --ctab
  >>     /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz
  >>     --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
  >>
  >>     It gives me the right regions for subcortical structures but it
  >>     looks like it uses the standard FS parcellation with my labels
  >>     for the cortical parcellations (only 93 cortical regions instead
  >>     of 210).
  >>
  >>     If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz
  >>     --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
  >>     --no-xcerseg I get all my 210 cortical parcellations but the
  >>     standard FS subcortical segmentations.
  >>
  >>     How can I use both in one gtmseg so that I can proceed with it
  >>     doing my PET analysis in PETSurfer? It is not totally clear for
  >>     me what to merge using xcerebralseg.
  >>
  >>     Thanks a lot!
  >>
  >>     On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D.
  >>     mailto:dgr...@mgh.harvard.edu>> wrote:
  >>
  >>         It gets the subcortical from apas+head.mgz which gets created
  >>         along the
  >>         way by xcerebralseg. You can create your own with
  >>         xcerebralseg by
  >>         specifying your volume as the mergevol. I think this will
  >>         work, but I'm
  >>         not sure. I'm assuming you've used the GCA to create your own
  >>         subcortical seg for the given subject
  >>
  >>         On 11/5/19 1:06 PM, Boris Rauchmann wrote:
  >>         >
  >>         > External Email - Use Caution
  >>         >
  >>         > I just realized that the above mentioned command (gtmseg
  >>         --s XYZ --o
  >>         > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
  >>         > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
  >>         --no-xcerseg)
  >>         > gives me only the cortical segmentation. Is there any way
  >>         to also
  >>         > include the subcortical segmentation based on my individual
  >>         atlas? I
  >>         > also have an 

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Thanks. unfortunately I get an error message when I use the --aseg flag for
BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get:
ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz

The file BN_Atlas_subcotex.mgz was created using:
mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
$SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz

Best,
Boris

On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your
> subcortical ROIs added? If so, you can try merging it with the aparc, eg,
>
> mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o
> aparc+BN_Atlas_subcotex.mgz
>
> Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then
> run gtmseg as you have done below.
>
> Let me know if that works
> doug
>
>
> On 12/2/19 1:18 PM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > In this example tried it with only the subcortical segmentations from
> > my atlas. Please find the logfile attached. It gives me back: "tissue
> > type is not set" but I set it to 2 in the LUT.txt
> >
> > In principle look the following commands right to you?
> >
> > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
> > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
> >
> > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
> > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
> >
> > Ideally I would have a gtmseg with both, the subcortical and the
> > cortical structures, but only the subcortical would also be fine as
> > long as I can get  mri_gtmpvc running on it.
> >
> > Thanks,
> > Boris
> >
> > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > Can you send the log file for each of the gtmseg runs?
> >
> > On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Thank you! I have a gca for subcortical  and two gcs (lh/rh) for
> >> cortical structures.
> >> I created an annot (rh/lh) and a mgz using mris_ca_label
> >> and mri_ca_label for parcellation/segmentation stats.
> >>
> >> For the PET analysis I have the following problem:
> >>
> >> If I use this command: gtmseg --s test --o test.mgz --ctab
> >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz
> >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
> >>
> >> It gives me the right regions for subcortical structures but it
> >> looks like it uses the standard FS parcellation with my labels
> >> for the cortical parcellations (only 93 cortical regions instead
> >> of 210).
> >>
> >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz
> >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
> >> --no-xcerseg I get all my 210 cortical parcellations but the
> >> standard FS subcortical segmentations.
> >>
> >> How can I use both in one gtmseg so that I can proceed with it
> >> doing my PET analysis in PETSurfer? It is not totally clear for
> >> me what to merge using xcerebralseg.
> >>
> >> Thanks a lot!
> >>
> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D.
> >> mailto:dgr...@mgh.harvard.edu>> wrote:
> >>
> >> It gets the subcortical from apas+head.mgz which gets created
> >> along the
> >> way by xcerebralseg. You can create your own with
> >> xcerebralseg by
> >> specifying your volume as the mergevol. I think this will
> >> work, but I'm
> >> not sure. I'm assuming you've used the GCA to create your own
> >> subcortical seg for the given subject
> >>
> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
> >> >
> >> > External Email - Use Caution
> >> >
> >> > I just realized that the above mentioned command (gtmseg
> >> --s XYZ --o
> >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> >> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> >> --no-xcerseg)
> >> > gives me only the cortical segmentation. Is there any way
> >> to also
> >> > include the subcortical segmentation based on my individual
> >> atlas? I
> >> > also have an Atlas_subcortex.gca file available.
> >> >
> >> > Best,
> >> > Boris
> >> >
> >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
> >> > mailto:dgr...@mgh.harvard.edu>
> >>  >> >> wrote:
> >> >
> >> > There is no cut off for the minimum size. As it gets
> >> smaller, the PVC
> >> > noise amplification will become bigger (it also 

Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your 
subcortical ROIs added? If so, you can try merging it with the aparc, eg,

mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o 
aparc+BN_Atlas_subcotex.mgz

Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then 
run gtmseg as you have done below.

Let me know if that works
doug


On 12/2/19 1:18 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> In this example tried it with only the subcortical segmentations from 
> my atlas. Please find the logfile attached. It gives me back: "tissue 
> type is not set" but I set it to 2 in the LUT.txt
>
> In principle look the following commands right to you?
>
> xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m 
> BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
>
> gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab 
> subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
>
> Ideally I would have a gtmseg with both, the subcortical and the 
> cortical structures, but only the subcortical would also be fine as 
> long as I can get  mri_gtmpvc running on it.
>
> Thanks,
> Boris
>
> On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Can you send the log file for each of the gtmseg runs?
>
> On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
>>
>> External Email - Use Caution
>>
>> Thank you! I have a gca for subcortical  and two gcs (lh/rh) for
>> cortical structures.
>> I created an annot (rh/lh) and a mgz using mris_ca_label
>> and mri_ca_label for parcellation/segmentation stats.
>>
>> For the PET analysis I have the following problem:
>>
>> If I use this command: gtmseg --s test --o test.mgz --ctab
>> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz
>> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
>>
>> It gives me the right regions for subcortical structures but it
>> looks like it uses the standard FS parcellation with my labels
>> for the cortical parcellations (only 93 cortical regions instead
>> of 210).
>>
>> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz
>> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
>> --no-xcerseg I get all my 210 cortical parcellations but the
>> standard FS subcortical segmentations.
>>
>> How can I use both in one gtmseg so that I can proceed with it
>> doing my PET analysis in PETSurfer? It is not totally clear for
>> me what to merge using xcerebralseg.
>>
>> Thanks a lot!
>>
>> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D.
>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>
>> It gets the subcortical from apas+head.mgz which gets created
>> along the
>> way by xcerebralseg. You can create your own with
>> xcerebralseg by
>> specifying your volume as the mergevol. I think this will
>> work, but I'm
>> not sure. I'm assuming you've used the GCA to create your own
>> subcortical seg for the given subject
>>
>> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
>> >
>> > External Email - Use Caution
>> >
>> > I just realized that the above mentioned command (gtmseg
>> --s XYZ --o
>> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
>> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
>> --no-xcerseg)
>> > gives me only the cortical segmentation. Is there any way
>> to also
>> > include the subcortical segmentation based on my individual
>> atlas? I
>> > also have an Atlas_subcortex.gca file available.
>> >
>> > Best,
>> > Boris
>> >
>> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>
>> > >> wrote:
>> >
>> >     There is no cut off for the minimum size. As it gets
>> smaller, the PVC
>> >     noise amplification will become bigger (it also depends
>> on the
>> >     shape as
>> >     well).
>> >
>> >     I think the --no-xcerseg is the right way to go now
>> >
>> >     On 8/13/19 11:00 AM, Boris Rauchmann wrote:
>> >     >
>> >     > External Email - Use Caution
>> >     >
>> >     > Thank you for your prompt answer - the command
>> worked. This is the
>> >     > atlas mentioned:
>> http://atlas.brainnetome.org/brainnetome.html
>> 
>> >     > What is approximately the smallest possible segment
>> when using PVC?
>> >     > Also, does the exclusion of extracerebral structures
>> harm? I
>> >     used that
>> 

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

In this example tried it with only the subcortical segmentations from my
atlas. Please find the logfile attached. It gives me back: "tissue type is
not set" but I set it to 2 in the LUT.txt

In principle look the following commands right to you?

xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca

gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz

Ideally I would have a gtmseg with both, the subcortical and the cortical
structures, but only the subcortical would also be fine as long as I can
get  mri_gtmpvc running on it.

Thanks,
Boris

On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Can you send the log file for each of the gtmseg runs?
>
> On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
> Thank you! I have a gca for subcortical  and two gcs (lh/rh) for cortical
> structures.
> I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label
> for parcellation/segmentation stats.
>
> For the PET analysis I have the following problem:
>
> If I use this command: gtmseg --s test --o test.mgz --ctab
> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot
> BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
>
> It gives me the right regions for subcortical structures but it looks like
> it uses the standard FS parcellation with my labels for the cortical
> parcellations (only 93 cortical regions instead of 210).
>
> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot
> BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my
> 210 cortical parcellations but the standard FS subcortical segmentations.
>
> How can I use both in one gtmseg so that I can proceed with it doing my
> PET analysis in PETSurfer? It is not totally clear for me what to merge
> using xcerebralseg.
>
> Thanks a lot!
>
> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> It gets the subcortical from apas+head.mgz which gets created along the
>> way by xcerebralseg. You can create your own with xcerebralseg by
>> specifying your volume as the mergevol. I think this will work, but I'm
>> not sure. I'm assuming you've used the GCA to create your own
>> subcortical seg for the given subject
>>
>> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
>> >
>> > External Email - Use Caution
>> >
>> > I just realized that the above mentioned command (gtmseg --s XYZ --o
>> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
>> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg)
>> > gives me only the cortical segmentation. Is there any way to also
>> > include the subcortical segmentation based on my individual atlas? I
>> > also have an Atlas_subcortex.gca file available.
>> >
>> > Best,
>> > Boris
>> >
>> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>> >
>> > There is no cut off for the minimum size. As it gets smaller, the
>> PVC
>> > noise amplification will become bigger (it also depends on the
>> > shape as
>> > well).
>> >
>> > I think the --no-xcerseg is the right way to go now
>> >
>> > On 8/13/19 11:00 AM, Boris Rauchmann wrote:
>> > >
>> > > External Email - Use Caution
>> > >
>> > > Thank you for your prompt answer - the command worked. This is the
>> > > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
>> > > What is approximately the smallest possible segment when using
>> PVC?
>> > > Also, does the exclusion of extracerebral structures harm? I
>> > used that
>> > > flag because it complained:
>> > >
>> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
>> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
>> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
>> > > but you must indicate whether to use what is there (--no-xcerseg)
>> > > or create a new one and overwrite what is there (--xcerseg)
>> > > or specify your own headseg (--head)
>> > >
>> > > and did not want to override my apas+head.mgz
>> > >
>> > > Thanks,
>> > > Boris
>> > >
>> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
>> > > mailto:dgr...@mgh.harvard.edu>
>> > >>
>> > wrote:
>> > >
>> > > I don't know what the Brainnetome is, but it looks like you
>> have
>> > > it in
>> > > annotation form. I think that command should work. Why are
>> > you using
>> > > --no-xcerseg? This will cause it to not include extracerebral
>> > > structures. Also note that you cannot use arbitrarily small
>> > segments
>> > > when doing PVC.
>> > >
>> >  

Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

Can you send the log file for each of the gtmseg runs?

On 11/26/2019 1:09 PM, Boris Rauchmann wrote:

External Email - Use Caution

Thank you! I have a gca for subcortical  and two gcs (lh/rh) for cortical 
structures.
I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label for 
parcellation/segmentation stats.

For the PET analysis I have the following problem:

If I use this command: gtmseg --s test --o test.mgz --ctab 
/xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot 
BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'

It gives me the right regions for subcortical structures but it looks like it 
uses the standard FS parcellation with my labels for the cortical parcellations 
(only 93 cortical regions instead of 210).

If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot 
BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my 210 
cortical parcellations but the standard FS subcortical segmentations.

How can I use both in one gtmseg so that I can proceed with it doing my PET 
analysis in PETSurfer? It is not totally clear for me what to merge using 
xcerebralseg.

Thanks a lot!

On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
It gets the subcortical from apas+head.mgz which gets created along the
way by xcerebralseg. You can create your own with xcerebralseg by
specifying your volume as the mergevol. I think this will work, but I'm
not sure. I'm assuming you've used the GCA to create your own
subcortical seg for the given subject

On 11/5/19 1:06 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> I just realized that the above mentioned command (gtmseg --s XYZ --o
> BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg)
> gives me only the cortical segmentation. Is there any way to also
> include the subcortical segmentation based on my individual atlas? I
> also have an Atlas_subcortex.gca file available.
>
> Best,
> Boris
>
> On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu> 
> >> wrote:
>
> There is no cut off for the minimum size. As it gets smaller, the PVC
> noise amplification will become bigger (it also depends on the
> shape as
> well).
>
> I think the --no-xcerseg is the right way to go now
>
> On 8/13/19 11:00 AM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > Thank you for your prompt answer - the command worked. This is the
> > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
> > What is approximately the smallest possible segment when using PVC?
> > Also, does the exclusion of extracerebral structures harm? I
> used that
> > flag because it complained:
> >
> > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
> > but you must indicate whether to use what is there (--no-xcerseg)
> > or create a new one and overwrite what is there (--xcerseg)
> > or specify your own headseg (--head)
> >
> > and did not want to override my apas+head.mgz
> >
> > Thanks,
> > Boris
> >
> > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu> 
> >
>  
>  wrote:
> >
> > I don't know what the Brainnetome is, but it looks like you have
> > it in
> > annotation form. I think that command should work. Why are
> you using
> > --no-xcerseg? This will cause it to not include extracerebral
> > structures. Also note that you cannot use arbitrarily small
> segments
> > when doing PVC.
> >
> > On 8/13/19 10:26 AM, Boris Rauchmann wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Dear all,
> > >
> > > my intention is to use the Brainnetome Atlas
> > parcellation/segmentation
> > > in PETSurfer to obtain PVC corrected SUVRs for the atlas
> ROIs. I
> > used:
> > >
> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot
> BN_Atlas.annot --ctab
> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> --no-xcerseg
> > >
> > > Is this the right approach to obtain a high resolution
> > segmentation to
> > > run PVC methods?
> > >
> > > Thanks,
> > > Boris
> > >
> > > ___
> > > 

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Thank you! I have a gca for subcortical  and two gcs (lh/rh) for cortical
structures.
I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label
for parcellation/segmentation stats.

For the PET analysis I have the following problem:

If I use this command: gtmseg --s test --o test.mgz --ctab
/xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot
BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'

It gives me the right regions for subcortical structures but it looks like
it uses the standard FS parcellation with my labels for the cortical
parcellations (only 93 cortical regions instead of 210).

If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot
BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my
210 cortical parcellations but the standard FS subcortical segmentations.

How can I use both in one gtmseg so that I can proceed with it doing my PET
analysis in PETSurfer? It is not totally clear for me what to merge using
xcerebralseg.

Thanks a lot!

On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> It gets the subcortical from apas+head.mgz which gets created along the
> way by xcerebralseg. You can create your own with xcerebralseg by
> specifying your volume as the mergevol. I think this will work, but I'm
> not sure. I'm assuming you've used the GCA to create your own
> subcortical seg for the given subject
>
> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > I just realized that the above mentioned command (gtmseg --s XYZ --o
> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg)
> > gives me only the cortical segmentation. Is there any way to also
> > include the subcortical segmentation based on my individual atlas? I
> > also have an Atlas_subcortex.gca file available.
> >
> > Best,
> > Boris
> >
> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > There is no cut off for the minimum size. As it gets smaller, the PVC
> > noise amplification will become bigger (it also depends on the
> > shape as
> > well).
> >
> > I think the --no-xcerseg is the right way to go now
> >
> > On 8/13/19 11:00 AM, Boris Rauchmann wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Thank you for your prompt answer - the command worked. This is the
> > > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
> > > What is approximately the smallest possible segment when using PVC?
> > > Also, does the exclusion of extracerebral structures harm? I
> > used that
> > > flag because it complained:
> > >
> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
> > > but you must indicate whether to use what is there (--no-xcerseg)
> > > or create a new one and overwrite what is there (--xcerseg)
> > > or specify your own headseg (--head)
> > >
> > > and did not want to override my apas+head.mgz
> > >
> > > Thanks,
> > > Boris
> > >
> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
> > > mailto:dgr...@mgh.harvard.edu>
> > >>
> > wrote:
> > >
> > > I don't know what the Brainnetome is, but it looks like you
> have
> > > it in
> > > annotation form. I think that command should work. Why are
> > you using
> > > --no-xcerseg? This will cause it to not include extracerebral
> > > structures. Also note that you cannot use arbitrarily small
> > segments
> > > when doing PVC.
> > >
> > > On 8/13/19 10:26 AM, Boris Rauchmann wrote:
> > > >
> > > > External Email - Use Caution
> > > >
> > > > Dear all,
> > > >
> > > > my intention is to use the Brainnetome Atlas
> > > parcellation/segmentation
> > > > in PETSurfer to obtain PVC corrected SUVRs for the atlas
> > ROIs. I
> > > used:
> > > >
> > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot
> > BN_Atlas.annot --ctab
> > > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> > --no-xcerseg
> > > >
> > > > Is this the right approach to obtain a high resolution
> > > segmentation to
> > > > run PVC methods?
> > > >
> > > > Thanks,
> > > > Boris
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > 

Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

It gets the subcortical from apas+head.mgz which gets created along the 
way by xcerebralseg. You can create your own with xcerebralseg by 
specifying your volume as the mergevol. I think this will work, but I'm 
not sure. I'm assuming you've used the GCA to create your own 
subcortical seg for the given subject

On 11/5/19 1:06 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> I just realized that the above mentioned command (gtmseg --s XYZ --o 
> BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab 
> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) 
> gives me only the cortical segmentation. Is there any way to also 
> include the subcortical segmentation based on my individual atlas? I 
> also have an Atlas_subcortex.gca file available.
>
> Best,
> Boris
>
> On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> There is no cut off for the minimum size. As it gets smaller, the PVC
> noise amplification will become bigger (it also depends on the
> shape as
> well).
>
> I think the --no-xcerseg is the right way to go now
>
> On 8/13/19 11:00 AM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > Thank you for your prompt answer - the command worked. This is the
> > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
> > What is approximately the smallest possible segment when using PVC?
> > Also, does the exclusion of extracerebral structures harm? I
> used that
> > flag because it complained:
> >
> > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
> > but you must indicate whether to use what is there (--no-xcerseg)
> > or create a new one and overwrite what is there (--xcerseg)
> > or specify your own headseg (--head)
> >
> > and did not want to override my apas+head.mgz
> >
> > Thanks,
> > Boris
> >
> > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>
> >>
> wrote:
> >
> >     I don't know what the Brainnetome is, but it looks like you have
> >     it in
> >     annotation form. I think that command should work. Why are
> you using
> >     --no-xcerseg? This will cause it to not include extracerebral
> >     structures. Also note that you cannot use arbitrarily small
> segments
> >     when doing PVC.
> >
> >     On 8/13/19 10:26 AM, Boris Rauchmann wrote:
> >     >
> >     > External Email - Use Caution
> >     >
> >     > Dear all,
> >     >
> >     > my intention is to use the Brainnetome Atlas
> >     parcellation/segmentation
> >     > in PETSurfer to obtain PVC corrected SUVRs for the atlas
> ROIs. I
> >     used:
> >     >
> >     > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot
> BN_Atlas.annot --ctab
> >     > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> --no-xcerseg
> >     >
> >     > Is this the right approach to obtain a high resolution
> >     segmentation to
> >     > run PVC methods?
> >     >
> >     > Thanks,
> >     > Boris
> >     >
> >     > ___
> >     > Freesurfer mailing list
> >     > Freesurfer@nmr.mgh.harvard.edu
> 
> >      >
> >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >     ___
> >     Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
>  >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

I just realized that the above mentioned command (gtmseg --s XYZ --o
BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
'/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) gives
me only the cortical segmentation. Is there any way to also include the
subcortical segmentation based on my individual atlas? I also have an
Atlas_subcortex.gca file available.

Best,
Boris

On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> There is no cut off for the minimum size. As it gets smaller, the PVC
> noise amplification will become bigger (it also depends on the shape as
> well).
>
> I think the --no-xcerseg is the right way to go now
>
> On 8/13/19 11:00 AM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > Thank you for your prompt answer - the command worked. This is the
> > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
> > What is approximately the smallest possible segment when using PVC?
> > Also, does the exclusion of extracerebral structures harm? I used that
> > flag because it complained:
> >
> > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
> > but you must indicate whether to use what is there (--no-xcerseg)
> > or create a new one and overwrite what is there (--xcerseg)
> > or specify your own headseg (--head)
> >
> > and did not want to override my apas+head.mgz
> >
> > Thanks,
> > Boris
> >
> > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > I don't know what the Brainnetome is, but it looks like you have
> > it in
> > annotation form. I think that command should work. Why are you using
> > --no-xcerseg? This will cause it to not include extracerebral
> > structures. Also note that you cannot use arbitrarily small segments
> > when doing PVC.
> >
> > On 8/13/19 10:26 AM, Boris Rauchmann wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Dear all,
> > >
> > > my intention is to use the Brainnetome Atlas
> > parcellation/segmentation
> > > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I
> > used:
> > >
> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg
> > >
> > > Is this the right approach to obtain a high resolution
> > segmentation to
> > > run PVC methods?
> > >
> > > Thanks,
> > > Boris
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Re: [Freesurfer] (no subject)

[Nader Razmara]

External Email - Use Caution

Thanks alot lilla.
Nader

On Tue, 29 Oct 2019, 19:37 Lilla Zollei 
> Our default setting to run mrri_cvs_register on our cluster is to use
> 35gb.
> Lilla
>
> On Tue, 29 Oct 2019, Nader Razmara wrote:
>
> >
> > Hi expertsI use freesurfer vm 5.3 on oracle vb 6 with 8 GB ram.
> > When i use mri_cvs_register as:
> > mri_cvs_register --mov subjid --mni or
> > mri_cvs_register --mov subjid --template subjid in both cases it stops
> in step 2 by diffrent errors. I asked zollei this problem and she sujest
> that it is ram problem.
> > My question is:
> > If it is true. How many ram this command needs?
> > Thanks
> > Nader
> > Phd student in medical engineering
> > Alzheimer research project
> >
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Re: [Freesurfer] (no subject)

[Lilla Zollei]

Our default setting to run mrri_cvs_register on our cluster is to use 
35gb.

Lilla

On Tue, 29 Oct 2019, Nader Razmara wrote:



Hi expertsI use freesurfer vm 5.3 on oracle vb 6 with 8 GB ram.
When i use mri_cvs_register as:
mri_cvs_register --mov subjid --mni or 
mri_cvs_register --mov subjid --template subjid in both cases it stops in step 
2 by diffrent errors. I asked zollei this problem and she sujest that it is ram 
problem.
My question is:
If it is true. How many ram this command needs?
Thanks 
Nader
Phd student in medical engineering
Alzheimer research project


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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Alright, thanks!

On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> There is no cut off for the minimum size. As it gets smaller, the PVC
> noise amplification will become bigger (it also depends on the shape as
> well).
>
> I think the --no-xcerseg is the right way to go now
>
> On 8/13/19 11:00 AM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > Thank you for your prompt answer - the command worked. This is the
> > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
> > What is approximately the smallest possible segment when using PVC?
> > Also, does the exclusion of extracerebral structures harm? I used that
> > flag because it complained:
> >
> > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
> > but you must indicate whether to use what is there (--no-xcerseg)
> > or create a new one and overwrite what is there (--xcerseg)
> > or specify your own headseg (--head)
> >
> > and did not want to override my apas+head.mgz
> >
> > Thanks,
> > Boris
> >
> > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > I don't know what the Brainnetome is, but it looks like you have
> > it in
> > annotation form. I think that command should work. Why are you using
> > --no-xcerseg? This will cause it to not include extracerebral
> > structures. Also note that you cannot use arbitrarily small segments
> > when doing PVC.
> >
> > On 8/13/19 10:26 AM, Boris Rauchmann wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Dear all,
> > >
> > > my intention is to use the Brainnetome Atlas
> > parcellation/segmentation
> > > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I
> > used:
> > >
> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg
> > >
> > > Is this the right approach to obtain a high resolution
> > segmentation to
> > > run PVC methods?
> > >
> > > Thanks,
> > > Boris
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
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Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

There is no cut off for the minimum size. As it gets smaller, the PVC 
noise amplification will become bigger (it also depends on the shape as 
well).

I think the --no-xcerseg is the right way to go now

On 8/13/19 11:00 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Thank you for your prompt answer - the command worked. This is the 
> atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
> What is approximately the smallest possible segment when using PVC?
> Also, does the exclusion of extracerebral structures harm? I used that 
> flag because it complained:
>
> gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab 
> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
> but you must indicate whether to use what is there (--no-xcerseg)
> or create a new one and overwrite what is there (--xcerseg)
> or specify your own headseg (--head)
>
> and did not want to override my apas+head.mgz
>
> Thanks,
> Boris
>
> On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> I don't know what the Brainnetome is, but it looks like you have
> it in
> annotation form. I think that command should work. Why are you using
> --no-xcerseg? This will cause it to not include extracerebral
> structures. Also note that you cannot use arbitrarily small segments
> when doing PVC.
>
> On 8/13/19 10:26 AM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > Dear all,
> >
> > my intention is to use the Brainnetome Atlas
> parcellation/segmentation
> > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I
> used:
> >
> > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg
> >
> > Is this the right approach to obtain a high resolution
> segmentation to
> > run PVC methods?
> >
> > Thanks,
> > Boris
> >
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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

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Thank you for your prompt answer - the command worked. This is the atlas
mentioned: http://atlas.brainnetome.org/brainnetome.html
What is approximately the smallest possible segment when using PVC?
Also, does the exclusion of extracerebral structures harm? I used that flag
because it complained:

gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
'/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
but you must indicate whether to use what is there (--no-xcerseg)
or create a new one and overwrite what is there (--xcerseg)
or specify your own headseg (--head)

and did not want to override my apas+head.mgz

Thanks,
Boris

On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> I don't know what the Brainnetome is, but it looks like you have it in
> annotation form. I think that command should work. Why are you using
> --no-xcerseg? This will cause it to not include extracerebral
> structures. Also note that you cannot use arbitrarily small segments
> when doing PVC.
>
> On 8/13/19 10:26 AM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > Dear all,
> >
> > my intention is to use the Brainnetome Atlas parcellation/segmentation
> > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used:
> >
> > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg
> >
> > Is this the right approach to obtain a high resolution segmentation to
> > run PVC methods?
> >
> > Thanks,
> > Boris
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

I don't know what the Brainnetome is, but it looks like you have it in 
annotation form. I think that command should work. Why are you using 
--no-xcerseg? This will cause it to not include extracerebral 
structures. Also note that you cannot use arbitrarily small segments 
when doing PVC.

On 8/13/19 10:26 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Dear all,
>
> my intention is to use the Brainnetome Atlas parcellation/segmentation 
> in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used:
>
> gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab 
> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg
>
> Is this the right approach to obtain a high resolution segmentation to 
> run PVC methods?
>
> Thanks,
> Boris
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] (no subject)

[许飞飞]

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I understand.

Thanks for your response, Feifei!


Bruce Fischl  于2019年7月16日周二 下午10:09写道：

> Hi Feifei
>
> we don't compute thickness using the method introudced by (MacDonald et
> al.2000). For that you can look at either our 1999 NeuroImage pair of
> papers or the 2000 PNAS paper.
>
> Essentially surface area is just the average area of the triangles that
> the
> vertex is attached to, and then volume is thickness times surface area.
> There are some details that Anderson Winkler worked out, but that is the
> core of it.
>
> cheers
> Bruce
>
>
> On Tue, 16 Jul 2019, 许飞飞 wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> >
> >
> >
> > I want to know how Freesufer to compute the volume and area at each
> vertex.
> > Are there any references? I just found the reference which introduces the
> > measure of thickness(MacDonald et al.2000).
> >
> >
> >
> > Any help with this would be greatly appreciated.
> >
> >
> >
> > Best regards, Feifei
> >
> >
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Re: [Freesurfer] (no subject)

[Bruce Fischl]

Hi Feifei

we don't compute thickness using the method introudced by (MacDonald et 
al.2000). For that you can look at either our 1999 NeuroImage pair of 
papers or the 2000 PNAS paper.


Essentially surface area is just the average area of the triangles that the 
vertex is attached to, and then volume is thickness times surface area. 
There are some details that Anderson Winkler worked out, but that is the 
core of it.


cheers
Bruce


On Tue, 16 Jul 2019, 许飞飞 wrote:



External Email - Use Caution

Dear Freesurfer experts,

 

I want to know how Freesufer to compute the volume and area at each vertex.
Are there any references? I just found the reference which introduces the
measure of thickness(MacDonald et al.2000).

 

Any help with this would be greatly appreciated.

 

Best regards, Feifei


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Re: [Freesurfer] Within-subject vertexwise correlation

[Greve, Douglas N.,Ph.D.]

I don't know. There is no way for me to answer that. It depends on the 
signal-to-noise of each of the modalities. You'll probably have to experiment a 
bit

On 6/22/2019 8:08 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

I effectively smoothed both modalities the same amount.

The question is whether I should or not smooth before calculating 
within-subject correlation?

Best,
Matthieu

Le sam. 22 juin 2019 à 02:14, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
I'm not sure that this is a question we can answer. If you do smooth, then you 
should smooth both modalities the same amount.

On 6/18/2019 10:12 PM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Dear FS experts,

I would like to compute within-subject correlation between two modalities based 
on vertexwise maps in fsaverage space. I wonder whether I have to smooth the 
normalized surface-based maps before computing vertexwise within-subject 
correlation?

I have noted that smoothing surface maps before computing correlation increases 
the output correlation value.

Thanks for your lights.

Best,
Matthieu



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Re: [Freesurfer] Within-subject vertexwise correlation

[Matthieu Vanhoutte]

External Email - Use Caution

I effectively smoothed both modalities the same amount.

The question is whether I should or not smooth before calculating
within-subject correlation?

Best,
Matthieu

Le sam. 22 juin 2019 à 02:14, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

> I'm not sure that this is a question we can answer. If you do smooth, then
> you should smooth both modalities the same amount.
>
> On 6/18/2019 10:12 PM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
> Dear FS experts,
>
> I would like to compute within-subject correlation between two modalities
> based on vertexwise maps in fsaverage space. I wonder whether I have to
> smooth the normalized surface-based maps before computing vertexwise
> within-subject correlation?
>
> I have noted that smoothing surface maps before computing correlation
> increases the output correlation value.
>
> Thanks for your lights.
>
> Best,
> Matthieu
>
> ___
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Re: [Freesurfer] Within-subject vertexwise correlation

[Greve, Douglas N.,Ph.D.]

I'm not sure that this is a question we can answer. If you do smooth, then you 
should smooth both modalities the same amount.

On 6/18/2019 10:12 PM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Dear FS experts,

I would like to compute within-subject correlation between two modalities based 
on vertexwise maps in fsaverage space. I wonder whether I have to smooth the 
normalized surface-based maps before computing vertexwise within-subject 
correlation?

I have noted that smoothing surface maps before computing correlation increases 
the output correlation value.

Thanks for your lights.

Best,
Matthieu



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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

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Alright, thanks I confused that. I already found a better way for my purposes. 
Im just running mri_gtmpvc using the flags —psf=0 and —no-tfe to get the non 
PVC subcortical SUVs.

> Am 17.05.2019 um 17:28 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> In mri_segstats, use --seg $SUBJECTS_DIR/xyz/mri/aparc+aseg.mgz 
> --ctab-default ...
> when you use --annot, you are saying that the input is on the surface.
> 
> On 5/17/2019 9:07 AM, Boris Rauchmann wrote:
>> External Email - Use Caution
>> 
>> Dear Freesurfer community,
>> 
>> I am trying to extract SUV values from sub-cortical segmentation or gtmseg I 
>> don t want to use any PVC. 
>> 
>> I used the following commands:
>> 
>> gtmseg --s xyz
>> 
>> then 
>> mri_coreg --s xyz --mov abetapet.nii.gz --reg abetapet.reg.lta
>> 
>> following
>> mri_vol2vol --mov abetapet.nii
>>  --reg abetapet.reg.lta --targ orig.mgz --o abetapet.sm00.nii.gz
>> and
>> 
>> mri_segstats  --annot
>>  xyz lh gtmseg --i abetapet.sm00.nii.gz --sum xyz_abeta.stats
>> 
>> resulting in this dimension mismatch error:
>> input 256 256 256
>>   seg   416 450 476
>> 
>> Is that the correct way for doing this analysis? any suggestions how to 
>> solve the mismatch error?
>> 
>> Thanks,
>> Boris
>> 
>> 
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Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

In mri_segstats, use --seg $SUBJECTS_DIR/xyz/mri/aparc+aseg.mgz --ctab-default 
...
when you use --annot, you are saying that the input is on the surface.

On 5/17/2019 9:07 AM, Boris Rauchmann wrote:

External Email - Use Caution

Dear Freesurfer community,

I am trying to extract SUV values from sub-cortical segmentation or gtmseg I 
don t want to use any PVC.

I used the following commands:

gtmseg --s xyz

then
mri_coreg --s xyz --mov abetapet.nii.gz --reg abetapet.reg.lta

following

mri_vol2vol --mov abetapet.nii --reg abetapet.reg.lta --targ orig.mgz --o 
abetapet.sm00.nii.gz

and


mri_segstats  --annot xyz lh gtmseg --i abetapet.sm00.nii.gz --sum 
xyz_abeta.stats

resulting in this dimension mismatch error:
input 256 256 256
  seg   416 450 476

Is that the correct way for doing this analysis? any suggestions how to solve 
the mismatch error?

Thanks,
Boris



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Re: [Freesurfer] (no subject)

[Giuliana Klencklen]

External Email - Use Caution

Yes, the theshold was the solution. Thanks again for your precious help!

On Fri, Mar 29, 2019 at 3:50 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> What threshold are you using in tksurfer? It should be the same as
> -log10(cwp), where cwp is the --cwp threshold you used in mri_glmfit-sim.
> If it is different, then it might not show all the cluster
>
> On 3/29/19 6:48 AM, Giuliana Klencklen wrote:
>
> External Email - Use Caution
> Hi FS experts,
>
> I use tksurfer (e.g., tksurfer fsaverage/ lh inflated -gray) to open the
> overlays (i.e., something.sig.cluster.mgh) I generated with the permutation
> simulation correction. It goes perfectly well for most of them expect for
> some, where the overlay does not show at all the significant clusters
> summarized in the something.sig.cluster.summary.
>
> I run the mri_glmfit-sim command again but the problem persists.
>
> Does anyone have a clue about what is going wrong?
>
> Many thanks,
> Giuliana Klencklen
>
>
> --
> Giuliana Klencklen, Ph.D.
>
> Helen Wills Neuroscience Institute
> University of California, Berkeley
> 118 Barker Hall
> Berkeley, CA 94720-3190
> 510-395-0040
> giuliana.klenck...@berkeley.edu
>
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-- 
Giuliana Klencklen, Ph.D.

Helen Wills Neuroscience Institute
University of California, Berkeley
118 Barker Hall
Berkeley, CA 94720-3190
510-395-0040
giuliana.klenck...@berkeley.edu
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Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

What threshold are you using in tksurfer? It should be the same as -log10(cwp), 
where cwp is the --cwp threshold you used in mri_glmfit-sim. If it is 
different, then it might not show all the cluster

On 3/29/19 6:48 AM, Giuliana Klencklen wrote:

External Email - Use Caution

Hi FS experts,

I use tksurfer (e.g., tksurfer fsaverage/ lh inflated -gray) to open the 
overlays (i.e., something.sig.cluster.mgh) I generated with the permutation 
simulation correction. It goes perfectly well for most of them expect for some, 
where the overlay does not show at all the significant clusters summarized in 
the something.sig.cluster.summary.

I run the mri_glmfit-sim command again but the problem persists.

Does anyone have a clue about what is going wrong?

Many thanks,
Giuliana Klencklen


--
Giuliana Klencklen, Ph.D.

Helen Wills Neuroscience Institute
University of California, Berkeley
118 Barker Hall
Berkeley, CA 94720-3190
510-395-0040
giuliana.klenck...@berkeley.edu



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Re: [Freesurfer] (no subject)

[Bruce Fischl]

do you mean the section in the left hemi temporal lobe (the lower right 
portion of your image)? That does not look like real white matter to me as 
it is adjacent to csf. Did you accidentally put some control points in gray 
matter (or csf)?


On Mon, 25 Mar 2019, Erika Portera wrote:



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Dear Freesurfer experts,

I have difficulty in introducing parts of white matter inside the superficial 
pial and white. I used
control points and modified the white matter volume but without resolution. Do 
you have any advice?

Thank you

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Re: [Freesurfer] Average subject

[Bruce Fischl]

yes, because the differences in their morphology don't change the average 
very much. You can try it both ways to verify this is true for your 
subjects.


cheers
Bruce


On Tue, 19 Feb 2019, 
Laboratorio de Neurociencia Funcional wrote:




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Thank, Bruce. So the final message is that I should use the same average 
subject to display results
of cortical thickness even when samples to be compared have highly different 
brain morphology. Is
that correct?

El lun., 18 feb. 2019 a las 23:37, Bruce Fischl () 
escribió:
  Hi Jose

  usually we don't need multiple averages (or study specific ones), which
  simplifies things considerably. Is there a reason you think you need one?
  We intentially use the gray/white boundary for this reason, which is
  insensitive to any possible cortical atrophy.

  cheers
  Bruce

  On Mon, 18 Feb 2019, Laboratorio de
  Neurociencia Funcional wrote:

  >
  > External Email - Use Caution
  >
  > Dear all,
  >
  > I am planning to run separate regression analysis with cortical 
thickness in two very
  different
  > populations (young and elderly subjects). Depending on results, it may 
happen that I
  am interested
  > in comparing regression slopes between the two groups. My question is: 
should I build
  one average
  > subject for each within-group regression analysis (one for young and 
another for
  elderly), and
  > another different average subject merging all subjects of the two 
samples to compare
  regression
  > slopes? Or I should preferably use only one average subjects with all 
subjects in all
  within and
  > between regression analysis?
  >
  > Many thanks in in advance.
  >
  > Best regards,
  > Jose
  >
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Re: [Freesurfer] Average subject

[Laboratorio de Neurociencia Funcional]

External Email - Use Caution

Thank, Bruce. So the final message is that I should use the same average
subject to display results of cortical thickness even when samples to be
compared have highly different brain morphology. Is that correct?

El lun., 18 feb. 2019 a las 23:37, Bruce Fischl ()
escribió:

> Hi Jose
>
> usually we don't need multiple averages (or study specific ones), which
> simplifies things considerably. Is there a reason you think you need one?
> We intentially use the gray/white boundary for this reason, which is
> insensitive to any possible cortical atrophy.
>
> cheers
> Bruce
>
> On Mon, 18 Feb 2019, Laboratorio de
> Neurociencia Funcional wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear all,
> >
> > I am planning to run separate regression analysis with cortical
> thickness in two very different
> > populations (young and elderly subjects). Depending on results, it may
> happen that I am interested
> > in comparing regression slopes between the two groups. My question is:
> should I build one average
> > subject for each within-group regression analysis (one for young and
> another for elderly), and
> > another different average subject merging all subjects of the two
> samples to compare regression
> > slopes? Or I should preferably use only one average subjects with all
> subjects in all within and
> > between regression analysis?
> >
> > Many thanks in in advance.
> >
> > Best regards,
> > Jose
> >
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Re: [Freesurfer] Average subject

[Bruce Fischl]

Hi Jose

usually we don't need multiple averages (or study specific ones), which 
simplifies things considerably. Is there a reason you think you need one? 
We intentially use the gray/white boundary for this reason, which is 
insensitive to any possible cortical atrophy.


cheers
Bruce

On Mon, 18 Feb 2019, Laboratorio de 
Neurociencia Funcional wrote:




External Email - Use Caution

Dear all,

I am planning to run separate regression analysis with cortical thickness in 
two very different
populations (young and elderly subjects). Depending on results, it may happen 
that I am interested
in comparing regression slopes between the two groups. My question is: should I 
build one average
subject for each within-group regression analysis (one for young and another 
for elderly), and
another different average subject merging all subjects of the two samples to 
compare regression
slopes? Or I should preferably use only one average subjects with all subjects 
in all within and
between regression analysis?

Many thanks in in advance.

Best regards,
Jose

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Re: [Freesurfer] (no subject)

[Bruce Fischl]

Hi Jordan

that is something you need to talk to your local sys admin about.

cheers
Bruce
On Mon, 4 
Feb 2019, Jordan Fowler wrote:




External Email - Use Caution

Hi Bruce,


How can I get read permission for that file/directory?


Jordan

_
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce
Fischl 
Sent: Monday, February 4, 2019 12:27:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] (no subject)  
Hi Jorgan

do you have read permission for that file/directory? It looks like not

cheers
Bruce



On Mon, 4 Feb 2019, Jordan Fowler wrote:

>
> External Email - Use Caution
>
> Here is the message displayed:
>
>
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME       /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR      /Applications/freesurfer/subjects
> MNI_DIR           /Applications/freesurfer/mni
> Jordans-MacBook-Air-2:~ jordanfowler$ > cp
> $FREESURFER_HOME/subjects/sample-001.mgz .
> -bash: /Applications/freesurfer/subjects/sample-001.mgz: Permission denied
>
>
>
>

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Re: [Freesurfer] (no subject)

[Jordan Fowler]

External Email - Use Caution

Hi Bruce,


How can I get read permission for that file/directory?


Jordan


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Monday, February 4, 2019 12:27:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] (no subject)

Hi Jorgan

do you have read permission for that file/directory? It looks like not

cheers
Bruce



On Mon, 4 Feb 2019, Jordan Fowler wrote:

>
> External Email - Use Caution
>
> Here is the message displayed:
>
>
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME   /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/subjects
> MNI_DIR   /Applications/freesurfer/mni
> Jordans-MacBook-Air-2:~ jordanfowler$ > cp
> $FREESURFER_HOME/subjects/sample-001.mgz .
> -bash: /Applications/freesurfer/subjects/sample-001.mgz: Permission denied
>
>
>
>
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Re: [Freesurfer] (no subject)

[Bruce Fischl]

Hi Jorgan

do you have read permission for that file/directory? It looks like not

cheers
Bruce



On Mon, 4 Feb 2019, Jordan Fowler wrote:



External Email - Use Caution

Here is the message displayed:


Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME       /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Applications/freesurfer/subjects
MNI_DIR           /Applications/freesurfer/mni
Jordans-MacBook-Air-2:~ jordanfowler$ > cp
$FREESURFER_HOME/subjects/sample-001.mgz .
-bash: /Applications/freesurfer/subjects/sample-001.mgz: Permission denied



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Re: [Freesurfer] Average-subject space

[Bruce Fischl]

Hi Sofia

what would that mean? Do you want to normalize the volumes? The volumes 
themselves are independent of any coordinate system, except for scaling. 
Normalizing usually isn't very useful since the goal of it would be to have 
them all be the same.


cheers
Bruce

On 
Wed, 30 Jan 2019, Sofia Rodriguez Penuela wrote:




External Email - Use Caution

Hi Freesurfer team!

How can I export the volumes of each subject to .nii in the space of the
average subject?

Thank you.


Sofía Rodríguez Peñuela.

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Re: [Freesurfer] (no subject)

[Emil H.J. Nijhuis]

External Email - Use Caution

Dear Ruopeng,

I tried the UpdateFreeview
<https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview?action=fullsearch=180=linkto%3A%22UpdateFreeview%22>
procedure below, however I received the error message:

>>
This application failed to start because it could not find or load the Qt
platform plugin "xcb"
in "".

Reinstalling the application may fix this problem.
Abort
<<

Any advice on how to solve this problem?

With best regards,

 Emil

Date: Mon, 7 Jan 2019 17:52:39 +0100
> From: "Larissa Bechtle" 
> Subject: Re: [Freesurfer] (no subject)
> To: "Freesurfer support list" 
> Message-ID:
>
>  >
>
> Content-Type: text/plain; charset="utf-8"
>
> External Email - Use Caution
>
> Hi Ruopeng,
>
> Thank you very much for your quick answer and advice. So I am going to
> update freeview!
> Thanks!
> Larissa
>
> Gesendet mit der WEB.DE Mail App
>
> Am 07.01.19 um 17:35 schrieb Ruopeng Wang
>
> > Hi Larissa,
> >
> > The latest development version of freeview supports drawing labels on
> > surface. You can take a look here on how to update freeview:
> >
> > https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
> >
> > In the latest version, you can draw paths on surface and use custom fill
> > to create/edit labels, just like in tksurfer.
> >
> > Best,
> > Ruopeng
> >
> > On 1/7/19 11:22 AM, Larissa Bechtle wrote:
> > >  External Email - Use Caution
> > >
> > > Hi everybody,
> > >
> > > after finishing my group analysis I am currently trying to run a ROI
> analysis.
> > > However I have some problems/general questions.
> > > I am trying to draw a ROI on fsaverage in order to use the
> mri_label2label command afterwards.
> > > I opened Freeview, clicked on "load surface" first and then chose
> lh.inflated_avg  (fsaverage -> surf) which worked fine but  I cant choose
> "New ROI" (in order to crate the ROI).
> > >
> > > So is it possible to draw a ROI when focussing only on the surface?
> And if this is the case why cant I? Did I chose the wrong file?
> > > I am really thankful for any help!!
> > >
> > > Larissa
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
>
> ___
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>
> End of Freesurfer Digest, Vol 179, Issue 11
> ***
>
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Re: [Freesurfer] (no subject)

[Larissa Bechtle]

External Email - Use Caution

Hi Ruopeng,

Thank you very much for your quick answer and advice. So I am going to update 
freeview! 
Thanks! 
Larissa

Gesendet mit der WEB.DE Mail App

Am 07.01.19 um 17:35 schrieb Ruopeng Wang

> Hi Larissa,
> 
> The latest development version of freeview supports drawing labels on 
> surface. You can take a look here on how to update freeview:
> 
> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
> 
> In the latest version, you can draw paths on surface and use custom fill 
> to create/edit labels, just like in tksurfer.
> 
> Best,
> Ruopeng
> 
> On 1/7/19 11:22 AM, Larissa Bechtle wrote:
> >  External Email - Use Caution
> >
> > Hi everybody,
> >   
> > after finishing my group analysis I am currently trying to run a ROI 
> > analysis.
> > However I have some problems/general questions.
> > I am trying to draw a ROI on fsaverage in order to use the mri_label2label 
> > command afterwards.
> > I opened Freeview, clicked on "load surface" first and then chose 
> > lh.inflated_avg  (fsaverage -> surf) which worked fine but  I cant choose 
> > "New ROI" (in order to crate the ROI).
> >   
> > So is it possible to draw a ROI when focussing only on the surface? And if 
> > this is the case why cant I? Did I chose the wrong file?
> > I am really thankful for any help!!
> >   
> > Larissa
> >   
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> ___
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Re: [Freesurfer] (no subject)

[Ruopeng Wang]

Hi Larissa,

The latest development version of freeview supports drawing labels on 
surface. You can take a look here on how to update freeview:

https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

In the latest version, you can draw paths on surface and use custom fill 
to create/edit labels, just like in tksurfer.

Best,
Ruopeng

On 1/7/19 11:22 AM, Larissa Bechtle wrote:
>  External Email - Use Caution
>
> Hi everybody,
>   
> after finishing my group analysis I am currently trying to run a ROI analysis.
> However I have some problems/general questions.
> I am trying to draw a ROI on fsaverage in order to use the mri_label2label 
> command afterwards.
> I opened Freeview, clicked on "load surface" first and then chose 
> lh.inflated_avg  (fsaverage -> surf) which worked fine but  I cant choose 
> "New ROI" (in order to crate the ROI).
>   
> So is it possible to draw a ROI when focussing only on the surface? And if 
> this is the case why cant I? Did I chose the wrong file?
> I am really thankful for any help!!
>   
> Larissa
>   
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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