Re: [Freesurfer] Tetrahedral mesh

2022-12-21 Thread Don Se 
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Ah, I see. However, I would like to get it for brain scans with a pathology
(a tumour).

2022-12-21, tr, 05:39 Douglas N. Greve  rašė:

> Why not samseg?
>
> On 12/20/2022 12:50 PM, Donatas Sederevičius wrote:
>
> External Email - Use Caution
> Hi, is there a tool to make a tetrahedral mesh of the brain from the MRI
> T1w image and/or its whole-brain segmentation? I need it for the finite
> elements method.
>
> -Don
>
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>  .
>
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Re: [Freesurfer] Tetrahedral mesh

2022-12-21 Thread Douglas N. Greve 
Not sure what it will do then. It will put vertices in that region. When 
you run samseg, add --save-mesh


On 12/21/2022 8:18 AM, Don Se wrote:


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Ah, I see. However, I would like to get it for brain scans with a 
pathology (a tumour).


2022-12-21, tr, 05:39 Douglas N. Greve  rašė:

Why not samseg?

On 12/20/2022 12:50 PM, Donatas Sederevičius wrote:


External Email - Use Caution

Hi, is there a tool to make a tetrahedral mesh of the brain from
the MRI T1w image and/or its whole-brain segmentation? I need it
for the finite elements method.

-Don

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Re: [Freesurfer] questions about mri_glmfit

2022-12-21 Thread James Brown 
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Dear Dr Greve, thank you so much for answers to my questions.
Regarding question 2, yes I meant leaving only columns I need, for instance
I am interested in lobes. I ran these commands on my data

# mri_annotation2label --subject subject --hemi lh --lobesStrict lobes
# mri_annotation2label --subject subject --hemi rh --lobesStrict lobes
# mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \
#   --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \
#   --annot lobes --base-offset 200 [--base-offset must be last arg]

then mri_segstats and I got the final stats file which contain data for the
lobes rois

3201wm-lh-frontal-lobe
3203wm-lh-cingulate-lobe
3204wm-lh-occiptal-lobe
3205wm-lh-temporal-lobe
3206wm-lh-parietal-lobe
3207wm-lh-insula-lobe

4201wm-rh-frontal-lobe
4203wm-rh-cingulate-lobe
4204wm-rh-occiptal-lobe
4205wm-rh-temporal-lobe
4206wm-rh-parietal-lobe
4207wm-rh-insula-lobe


My question is can I revise the spreadsheet from the output of
aparcstats2table or asegstats2table to keep the lobar ROIs above (8
columns) then feed that data to mri_glmfit?

On 12/20/2022 12:22 PM, James Brown wrote:

Dear Freesurfer experts,
I have 2 questions about the command mri_glmfit and I appreciate your help.
1- Are there any settings or flags that can be used in mri_glmfit to
restrict statistical comparison of surface based analysis to specific ROIs
rather than whole brain analysis. I would like to show the difference on
the brain surface in lobes rather than in sub lobar labels.

You can create a mask or label and feed it into mri_glmfit with --mask or
--label

2- I understand that the flag "--table" in command mri_glmfit allows for
feeding spreadsheets instead of images. Can we restrict the number of
columns in this spreadsheet to 8 columns for lobs (frontal, temporal,
occipital and parietal) left and right? Also, is there any way to generate
a statistical map from the spreadsheet statistics?

Remove the columns you don't want?

On Tue, Dec 20, 2022 at 12:22 PM James Brown  wrote:

> Dear Freesurfer experts,
> I have 2 questions about the command mri_glmfit and I appreciate your help.
> 1- Are there any settings or flags that can be used in mri_glmfit to
> restrict statistical comparison of surface based analysis to specific ROIs
> rather than whole brain analysis. I would like to show the difference on
> the brain surface in lobes rather than in sub lobar labels.
> 2- I understand that the flag "--table" in command mri_glmfit allows for
> feeding spreadsheets instead of images. Can we restrict the number of
> columns in this spreadsheet to 8 columns for lobs (frontal, temporal,
> occipital and parietal) left and right? Also, is there any way to generate
> a statistical map from the spreadsheet statistics?
>
> Thank you and happy holidays :)
> James
>
>
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[Freesurfer] Freesurfer question about recon-all

2022-12-21 Thread Rosalia Dacosta Aguayo 
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Dear Freesurfer group,

Could you tell me which is the flag I need to use to get all the brain
parcellation when I run recon-all? It seems I am getting the tables with
few volumes and I guess there is something wrong.

Best wishes and Merry Christmas,

Rosie
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Re: [Freesurfer] Freesurfer question about recon-all

2022-12-21 Thread Rosalia Dacosta Aguayo 
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Maybe is -qcache ?




On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo 
wrote:

> Dear Freesurfer group,
>
> Could you tell me which is the flag I need to use to get all the brain
> parcellation when I run recon-all? It seems I am getting the tables with
> few volumes and I guess there is something wrong.
>
> Best wishes and Merry Christmas,
>
> Rosie
>
>
>
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Re: [Freesurfer] Freesurfer question about recon-all

2022-12-21 Thread Douglas N. Greve 

what are  you not getting?

On 12/21/2022 10:11 AM, Rosalia Dacosta Aguayo wrote:


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Maybe is -qcache ?

*
*



On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo 
 wrote:


Dear Freesurfer group,

Could you tell me which is the flag I need to use to get all the
brain parcellation when I run recon-all? It seems I am getting the
tables with few volumes and I guess there is something wrong.

Best wishes and Merry Christmas,

Rosie

*
*


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Re: [Freesurfer] Freesurfer question about recon-all

2022-12-21 Thread Rosalia Dacosta Aguayo 
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Hi Douglas,

I am only getting the main volumes like putamen right and left, amygdala,
right and left...just gross anatomy.

Rosie




On Wed, Dec 21, 2022 at 4:32 PM Douglas N. Greve 
wrote:

> what are  you not getting?
>
> On 12/21/2022 10:11 AM, Rosalia Dacosta Aguayo wrote:
>
> External Email - Use Caution
> Maybe is -qcache ?
>
>
>
>
> On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo <
> rdacos...@gmail.com> wrote:
>
>> Dear Freesurfer group,
>>
>> Could you tell me which is the flag I need to use to get all the brain
>> parcellation when I run recon-all? It seems I am getting the tables with
>> few volumes and I guess there is something wrong.
>>
>> Best wishes and Merry Christmas,
>>
>> Rosie
>>
>>
>>
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Re: [Freesurfer] Freesurfer question about recon-all

2022-12-21 Thread Rosalia Dacosta Aguayo 
External Email - Use Caution

I do not get the cingulate, for example...




On Wed, Dec 21, 2022 at 4:35 PM Rosalia Dacosta Aguayo 
wrote:

> Hi Douglas,
>
> I am only getting the main volumes like putamen right and left, amygdala,
> right and left...just gross anatomy.
>
> Rosie
>
>
>
>
> On Wed, Dec 21, 2022 at 4:32 PM Douglas N. Greve 
> wrote:
>
>> what are  you not getting?
>>
>> On 12/21/2022 10:11 AM, Rosalia Dacosta Aguayo wrote:
>>
>> External Email - Use Caution
>> Maybe is -qcache ?
>>
>>
>>
>>
>> On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo <
>> rdacos...@gmail.com> wrote:
>>
>>> Dear Freesurfer group,
>>>
>>> Could you tell me which is the flag I need to use to get all the brain
>>> parcellation when I run recon-all? It seems I am getting the tables with
>>> few volumes and I guess there is something wrong.
>>>
>>> Best wishes and Merry Christmas,
>>>
>>> Rosie
>>>
>>>
>>>
>> ___
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>>  .
>>
>
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Re: [Freesurfer] mri_robust_template - MyMatrix::RotationMean Error

2022-12-21 Thread Huang, Yujing 
Hi Andrew,

Sorry for the late response. Copied below is the suggestions from Martin.

“
I looked at those images. A few points:

- bias fields seem to be very different, I think using --iscale helps a little 
here, if very high accuracy of the registration is important, one should do a 
bias field removal beforehand.

- manually setting the sat to anything between 5 and 8 also looked like it 
helps --sat 5 in robust register

- robust register can be used if only two time points are involved to register 
into a mid space using —halfdst halfmov and halfdstlta outputs you get those 
images and transforms. Only thing missing is the actual template image which 
for two time points is simply the average of the two images after alignment in 
the mid space (so probably mri_calc or some other tool can compute that average 
image if it is needed).

- Scalp is changing a lot here across time, not sure why. How far are these 
time points apart? What type of data (aging, disease, treatment) is this? There 
are also noticeable changes in the brain. Anyway, best results are when using 
the skull stripped images, it is also faster. In freesurfer we work with 
norm.mgz in the longitudinal pipeline which are both skull stripped an bias 
corrected.

- Finally, in robust_template I also get the error about deviation from 
rotation. For some reason, that I could not yet find out, the first 
registration of A to B is not perfectly a rigid transform (some small deviation 
from a rotation matrix, maybe very subtle shearing as the determinant is still 
very close to 1, so no scaling). This could be a numerical issue. Anyway 
increasing the threshold to 0.001 should fix this. Or did you get another error 
after that for this specific case?
“



From: Andrew Beaudin 
Sent: Wednesday, December 7, 2022 1:30 PM
To: Huang, Yujing ; Freesurfer support list 

Cc: Reuter, Martin,Ph.D. 
Subject: Re: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean 
Error


External Email - Use Caution
Hi Yujing,
 No problem at all.  I really appreciate yours, and now Martin's, help with 
this issue.  If you would like to start with dicoms, please let me know.

Again, thank you both for your help.

Andrew


Andrew Beaudin, PhD | Research Associate
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273


From: Huang, Yujing [mailto:yhuan...@mgh.harvard.edu]
Sent: Wednesday, December 7, 2022 at 10:27
To: Andrew Beaudin , 
Freesurfer support list 

Cc: Reuter, Martin,Ph.D. 

Subject: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

[△EXTERNAL]

Hi Andrew,

Sorry for the late response. I’m able to reproduce your error.

I have included Martin to the communication. He is the author of the program. 
He is going to take a look at your data.

Best,

Yujing



From: Andrew Beaudin 
Sent: Friday, November 25, 2022 3:25 PM
To: Huang, Yujing ; 
Freesurfer support list 

Subject: RE: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean 
Error


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Hi Huang,
  Thank you very much for your help with this.  Apologies for the delay.

  You should be able to retrieve sample images from the following link (expires 
on Dec. 2).  I have also included a brief word document at the link that 
includes some details of the nifti images.

https://uofc-my.sharepoint.com/:f:/g/personal/abeaudin_ucalgary_ca/EmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ


The command call I am using is:

mri_robust_template --mov 2001A_T1o_brain.nii.gz 2001B_T1o_brain.nii.mgz --lta 
2001A2template.lta 2001B2template.lta --average 1 --template 
2001_template.nii.gz --satit

  However, while troubleshooting I have also tried the following with no 
success:

1) using the --iscale flag - same MyMatrix::RotationMean Error (see below for 
log)
2) using --inittp 0 - results in a 'Segmentation fault'
3) using --average 0 - same MyMatrix::RotationMean Error
4) using Freesurfer v7.2 - same MyMatrix::RotationMean Error
5) running mri_robust_template call on Catalina and Big Sur systems with FS 
v6.0 - same MyMatrix::RotationMean Error.


Again, thank you for the help….and please le

[Freesurfer] HELP! PASSWORD TO UNZIP FS_7_2_0_ubuntu_18_04_06.ova

2022-12-21 Thread Ganeshkaran Mouralidaran 
External Email - Use Caution

Greetings,
I am writing regarding the request to grant the password to
unzip FS_7_2_0_ubuntu_18_04_06.ova file
Thanks and regards,
Ganeshkaran
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Re: [Freesurfer] lh.pial lh.pialT1n same file?

2022-12-21 Thread Huang, Yujing 
Hi Rene,

I don’t see any errors in your recon-all log.

I’m wondering if ‘ln -sf’ works on Mac.

Can you try the following:
1. cd to ‘surf’ directory
2. ln -sf lh.pial.T1 testlink
3. ls -l testlink
4. ls -lt ?h.pial* ?h.white* ?h*.sphere.reg

Can you send the output from those commands?

Yujing


From: Renew Andrade 
Sent: Tuesday, December 20, 2022 11:04 AM
To: Huang, Yujing 
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?


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andraderenew@andraderenew:/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25633_T1MPRAGE_1mm_reconall/surf$
  ls -l lh.pial*
-rwxr-xr-x 1 andraderenew andraderenew 4551861 ago 23 03:05 lh.pial.T1



This is all I have. Thanks for the help in advance.


On 20 Dec 2022, at 15:12, Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:

Hi Rene,

Can you send your recon-all.log? It is in the ‘scripts’ directory.

‘lh.pial’ should be created as a link to ‘lh.pial.T1’ if you are not processing 
T2/FLAIR.  If you go ‘surf’ directory, do ‘ls -l lh.pial*’, what does it shows?

Best,

Yujing

From: Renew Andrade mailto:andradere...@yahoo.com>>
Sent: Tuesday, December 20, 2022 1:23 AM
To: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>; 
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?


External Email - Use Caution
Dear Yujing:
I wasn’t aware that there was an answer to my email that’s the reason it took 
me a while to write back. But I answer here.
Yes I mean lh.pial.T1. I don’t have any other lh.pial. The recon-all command is 
properly correct like recon-all -all -i -s -openmp 8. Yes the freesurfer 
version is 7.1.1.

Best,
Rene Andrade.







Hi Rene,



Do you mean lh.pial.T1? Do you have any other lh.pial* files in the directory?

What is your recon-all command line? And can you also provide the Freesurfer

version you are running?



Best,



Yujing



-Original Message-

From: 
freesurfer-boun...@nmr.mgh.harvard.edu

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Renew Andrade

Sent: Tuesday, December 13, 2022 7:24 AM

To: freesurfer@nmr.mgh.harvard.edu

Subject: [Freesurfer] lh.pial lh.pialT1n same file?



External Email - Use Caution



Dear experts:



I am wondering if lh.pial and lh.pialT1 are the same files. I don’t have

lh.pial is that an error from recon-all? Should I rerun recon-all. Or just

autorecon-pial? Would that change anything?



Best,

Rene Andrade.



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***UNCHECKED*** [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Volumetric extraction from volumetric mask in MNI space

2022-12-21 Thread Beatriz Cavendish 
External Email - Use Caution

Hello,

I would like to know the step by step to obtain volume (mm3) from a
volumetric mask in the MNI space (follow the attached nifti file). I
checked the forum but the tutorials are for surface extraction and cortical
thickness.

Yours sincerely,

-- 
Beatriz Araújo Cavendish, MSc

PhD student | Psychologist

University of São Paulo

São Paulo/SP - Brazil


Cluster1_R.nii.gz
Description: GNU Zip compressed data


Cluster1_L.nii.gz
Description: GNU Zip compressed data
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Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Volumetric extraction from volumetric mask in MNI space

2022-12-21 Thread Douglas N. Greve 

Try
mri_segstats --seg Cluster1_R.nii.gz --id 1 --sum sum.R.dat
That will give you the number of voxels that have a value=1 times the 
size of the voxel (so the volume). It will not be in MNI space unless 
the nifti files you sent are in MNI space.



On 12/21/2022 5:42 PM, Beatriz Cavendish wrote:


External Email - Use Caution

Hello,

I would like to know the step by step to obtain volume (mm3) from a 
volumetric mask in the MNI space (follow the attached nifti file). I 
checked the forum but the tutorials are for surface extraction and 
cortical thickness.


Yours sincerely,

--
Beatriz Araújo Cavendish, MSc

PhD student | Psychologist

University of São Paulo

São Paulo/SP - Brazil


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