[Freesurfer] mri_watershed

[nima]

hi,
Under freesurfer, how can I force mri_watershed to create 5012 triangles
(ico 4) instead of 20480?
cheers
nima


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[Freesurfer] mathematica and freesurfer

[nima]

Hi,
Does anybody have (or know of) functions for reading freesurfer's surface
or curvature into Mathematica?


Nima
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[Freesurfer] color of faces of freesurfer's surfaces

[nima]

Hi,
I can read (in Matlab) the freesurfer's coordinates of vertices but can
not find how the colors are defined (i.e. colors of sulci versus gyri).
Where can I find this information?
best
Nima
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[Freesurfer] vertex neighbourhood

[nima]

hi surfers,
Imagine that I need to know what are the closest N vertices (let's say
n=100) to a given vertex (i mean two dimentionsal neighourhood on
surfaces) . Any idea how to do that? anybody has a written code for this?
cheers
nima
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[Freesurfer] midline errors in pial and white matter boundary

[nima]

Hi Guys,
In few recons, I  noitced that in the midline, pial and white matter
boundaries are not the way they are supposed to be; i.e., they sometimes
diverge toward the ventricles instead of following the midline and these
divergences are not symmetrical either.
I thought maybe I should add some cp...but that does not make sense
because in actuality there is not white matter there as it is underneath
the cortical gray matter...
Any suggestion?

The new version of the freesurfer fills the 3rd ventricle adjacent to the
fornices. Should I leave the fornices in? or I should clean it up like old
versions?

ps. is there any way to add control points for pial surface?

cheers
nima
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[Freesurfer] mgh2 stc

[nima]

Hi
Does anybody have a code to convert mgh format to stc?
best
Nima

Nima Dehghani MD.

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[Freesurfer] missing curvatures

[nima]

hi 
after "making final surfaces" i enountered something strange!
lh: "inflated" brain and "smoothwm" has no curvature but other surfaces
like orig va qshere are normal
rh: inflated brain has the curvature but other surfaces are normal
logfiles are shown below.
what is the prob?!?!?
any idea?
cheers
nimA



FOR LEFT HEMISPHERE "INFLATED":

"
env tksurferinterface=csurf patchname=
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/tksurfer -sleep_s2
lh inflated -tcl /tmp/TmpTclSurf.12210
MRISreadVertexPositions(/space/humpback/2/users/nima/csurf/sleep_s2/surf/lhorig):
surfaces differ.

No such file or directory
MRISreadOriginalProperties: could not read surface file
/space/humpback/2/users/nima/csurf/sleep_s2/surf/lh.orig
No such file or directory
Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkm_wrappers.tcl
Using libtclfsgdf.so
Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkUtils.tcl
Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
MRISreadNewCurvature: incompatible vertex number in file
/space/humpback/2/users/nima/csurf/sleep_s2/surf/lh.curv
surfer: current subjects dir: /space/humpback/2/users/nima/csurf
surfer: in subjects "scripts" dir
surfer: session root data dir ($session) set to:
surfer: /autofs/space/humpback_002/users/nima/csurf/sleep_s2
surfer: /space/humpback/2/users/nima/csurf/sleep_s2/mri/T1/COR-.info
surfer: vertices=125362, faces=250720
surfer: using interface
/space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tksurfer.new.tcl
Read /space/lyon/1/home/inverse/freesurfer_alpha/surface_labels.txt,
found 95 structures
tksurfer: run tcl script: /tmp/TmpTclSurf.12210
surfer: single buffered window
surfer: curvature read: min=0.00 max=0.00
"

ps. point is that lh.orig exists! so i do not know what it says that it
can not find it!

FOR LEFT HEMISPHERE "INFLATED":

"env tksurferinterface=csurf patchname=
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/tksurfer -sleep_s2
lh smoothwm -tcl /tmp/TmpTclSurf.12210
MRISreadVertexPositions(/space/humpback/2/users/nima/csurf/sleep_s2/surf/lhorig):
surfaces differ.

No such file or directory
MRISreadOriginalProperties: could not read surface file
/space/humpback/2/users/nima/csurf/sleep_s2/surf/lh.orig
No such file or directory
Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkm_wrappers.tcl
Using libtclfsgdf.so
Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkUtils.tcl
Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
MRISreadNewCurvature: incompatible vertex number in file
/space/humpback/2/users/nima/csurf/sleep_s2/surf/lh.curv
surfer: current subjects dir: /space/humpback/2/users/nima/csurf
surfer: in subjects "scripts" dir
surfer: session root data dir ($session) set to:
surfer: /autofs/space/humpback_002/users/nima/csurf/sleep_s2
surfer: /space/humpback/2/users/nima/csurf/sleep_s2/mri/T1/COR-.info
surfer: vertices=125362, faces=250720
surfer: using interface
/space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tksurfer.new.tcl
Read /space/lyon/1/home/inverse/freesurfer_alpha/surface_labels.txt,
found 95 structures
tksurfer: run tcl script: /tmp/TmpTclSurf.12210
surfer: single buffered window
surfer: curvature read: min=0.00 max=0.00"

ps. point is that lh.orig exists! so i do not know what it says that it
can not find it!


FOR RIGHT HEMISPHERE "INFLATED SURFACE":
ha/bin/Linux/tksurfer -sleep_s2 rh qsphere -tcl /tmp/TmpTclSurf.12210
mrisReadTriangleFile(/space/humpback/2/users/nima/csurf/sleep_s2/surf/rh.orig):
surface doesn't match
/space/humpback/2/users/nima/csurf/sleep_s2/surf/rh.qsphere

No such file or directory
mrisReadTriangleFile failed.

No such file or directory
MRISreadOriginalProperties: could not read surface file
/space/humpback/2/users/nima/csurf/sleep_s2/surf/rh.orig
No such file or directory
Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkm_wrappers.tcl
Using libtclfsgdf.so
Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkUtils.tcl
Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
MRISreadNewCurvature: incompatible vertex number in file
/space/humpback/2/users/nima/csurf/sleep_s2/surf/rh.curv
surfer: current subjects dir: /space/humpback/2/users/nima/csurf
surfer: in subjects "scripts" dir
surfer: session root data dir ($session) set to:
surfer: /autofs/space/humpback_002/users/nima/csurf/sleep_s2
surfer: /space/humpback/2/users/nima/csurf/sleep_s2/mri/T1/COR-.info
surfer: vertices=127844, faces=255756
surfer: using interface
/space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tksurfer.new.tcl
Read /space/lyon/1/home/inverse/freesurfer_alpha/surface_labels.txt,
found 95 structures
tksurfer: run tcl script: /tmp/TmpTclSurf.12210
surfer: 

[Freesurfer] question(s) about brain volume calculation

[Golchin, Nima]

I was wondering how FreeSurfer calculates brain volume.  Is volume calculated 
from the voxels included in brainmask.mgz, from the area inside the generated 
Pial surface, or from summing the aseg volume statistics?  Also, to exclude 
ventricular volume, do you just subtract the segmented ventricle label volume?  
I ask because I was wondering what freesurfer errors I should be concerned 
about most when looking at whole brain volume (pial surface including 
eye/skull, overzealous segmentation labeling, etc).  Also, how should I 
consider whole brain volume regarding the difficulties freesurfer has 
calculating the surface of the hippocampus.  Thanks for your help.  
-Nima
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[Freesurfer] Inquiry About Longitudinal Analysis Using recon-all-clinical.sh

[Taghizadeh Mortezaei, Nima]

Dear FreeSurfer Community,

I want to work on a longitudinal analysis with two time points (pre-treatment 
and post-treatment) and would like to follow the recommended longitudinal 
pipeline. However, I want to use recon-all-clinical.sh and I want to ask 
whether the commands and steps for recon-all-clinical.sh are the same as the 
standard recon-all longitudinal pipeline? Are there any modifications or 
additional considerations required when using this script for longitudinal 
processing?

I appreciate any guidance or documentation references that could help with this 
analysis.

Thank you for your time and support!

Nima

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[Freesurfer] Inquiry About Longitudinal Analysis Using recon-all-clinical.sh

[Taghizadeh Mortezaei, Nima]

Dear FreeSurfer Community,

I want to work on a longitudinal analysis with two time points (pre-treatment 
and post-treatment) and would like to follow the recommended longitudinal 
pipeline. However, I want to use recon-all-clinical.sh and I want to ask 
whether the commands and steps for recon-all-clinical.sh are the same as the 
standard recon-all longitudinal pipeline? Are there any modifications or 
additional considerations required when using this script for longitudinal 
processing?

I appreciate any guidance or documentation references that could help with this 
analysis.

Thank you for your time and support!

Nima

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[Freesurfer] Issue with Voxel Size Mismatch in Samseg-Long Pipeline

[Taghizadeh Mortezaei, Nima]

Dear FreeSurfer Team,
I am working with two timepoints for a subject and attempting to create a 
template for samseg-long using mri_robust_template. However, I encountered an 
error related to voxel size mismatch between the input images. Both timepoint 
images are T1W.
The command I ran is:

mri_robust_template --mov subject1_preRT.nii subject1_postRT.nii --template 
mean.mgz --satit --mapmov subject1_preRT_reg.mgz
subject1_postRT_reg.mgz


I received the following error:

ERROR: MultiRegistration::loadMovables: images have different voxel sizes.
  Currently not supported, maybe first make conform?
  Debug info: size(1) = 0.428571, 0.428571, 4.4   size(0) = 0.449219, 0.449219, 
5
error: Operation not permitted
error: MultiRegistration::loadMovables: voxel size is different 
subject1_postRT.nii.


>From what I understand, mri_robust_template does not support different voxel 
>sizes between input images. Would the recommended approach be to first 
>resample the images to the same voxel size using mri_convert --conform or 
>another method before running mri_robust_template?
Additionally, would this resampling introduce any potential biases that I 
should be aware of in a longitudinal analysis? If there is a better way to 
handle this issue, I would greatly appreciate your guidance.
Best regards,
Nima
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[Freesurfer] Identical values for different cingulate regions

[Taghizadeh Mortezaei, Nima]

Dear FreeSurfer developers and community,

I was reviewing the stats outputs of recon-all from multiple cases processed 
using FreeSurfer version 6.0.0, and I encountered an unusual issue. 
Unfortunately, I do not have access to the stats files, but based on the 
results provided in excel, I have noticed that the gray matter volumes for the 
caudal anterior cingulate and isthmus cingulate are identical within each 
hemisphere. (lh.caudal_anterior_cingulate = lh.isthmus_cingulate
rh.caudal_anterior_cingulate = rh.isthmus_cingulate). Also, the white matter 
volumes for the isthmus cingulate are also identical between hemispheres 
(lh.isthmus_cingulate = rh.isthmus_cingulate).
The consistent pattern across all cases and its limitation to the cingulate 
regions leads me to question whether this could be possible from an issue in 
the segmentation and parcellation processing, or if it might be due to errors 
during data transfer.

I would appreciate your guidance. Please let me know if additional details or 
context would help clarify this matter.

Thanks!
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Re: [Freesurfer] Issue with Right Hemisphere Segmentation/Parcellation

[Taghizadeh Mortezaei, Nima]

Thanks for your guidance. I already tried recon-all-clinical.sh; however, I was 
wondering why did this happen? Could it be related to resampling process or the 
orientation?

Thanks,
Nima

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Tuesday, January 28, 2025 12:41 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Issue with Right Hemisphere Segmentation/Parcellation

Try using recon-all-clinical.sh; it works a lot better on these thick slice data


On 1/28/2025 12:24 PM, Taghizadeh Mortezaei, Nima wrote:
Hello FreeSurfer Developers and Community,

I am working with an axial T1-weighted post-contrast MRI, with an original 
voxel size of 1×1×5.5 mm. I resampled this MRI in 3D Slicer using B-Spline 
interpolation and then saved it as a mgz file. After running recon-all on this 
resampled file, I noticed that the right hemisphere’s segmentation and 
parcellation are flawed. Also, considering the age and health situation of this 
patient, i believe the WM hypointensities are overestimated in the left 
hemisphere.

I am using the following version of FreeSurfer: 
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460.
The command line was:
recon-all -s 12th_recon_output -i input.mgz -all -parallel -openmp 12

I’ve attached the recon-all log file, a screenshot from Freeview to illustrate 
the issue, and mri_info file. I would greatly appreciate any guidance, 
troubleshooting advice, or suggestions on what might have gone wrong and how to 
correct this issue.

Thank you in advance for your help!

Best regards,
Nima



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[Freesurfer] Corpus Callosum Missing in SAMSEG Output

[Taghizadeh Mortezaei, Nima]

Dear FreeSurfer Support Team,

I am using FreeSurfer version 7.4.1 and recently ran SAMSEG on a subject’s MRI 
data. However, I noticed that the corpus callosum does not appear as a distinct 
label in the segmented structures. After reviewing the output files and label 
definitions, I was unable to find any explicit segmentation for the corpus 
callosum in the SAMSEG results.

Could you please clarify if the corpus callosum is included as a distinct 
structure in the default SAMSEG atlas? If not, is there a recommended approach 
to extract or segment the corpus callosum using SAMSEG?

Any guidance or suggestions would be greatly appreciated. Please let me know if 
additional details or files are needed for context.

Thank you for your time and support.

Best regards,
Nima Taghizadeh
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[Freesurfer] Issue with mri_histo_atlas_segment_fireants Command

[Taghizadeh Mortezaei, Nima]

Dear FreeSurfer Developers and Community,
I am trying to run Bayesian Segmentation with the Histological Atlas 
"NextBrain" in FreeSurfer. I have already downloaded and uncompressed the atlas 
into the ERC_bayesian_segmentation folder. However, when I attempt to proceed, 
I encounter the following error:
zsh: command not found: mri_histo_atlas_segment_fireants
I am using FreeSurfer version 
freesurfer-macOS-darwin_x86_64-8.0.0-beta-20241103-b8aacdc.
Could you please let me know if this command is supported in my version or if I 
am missing any setup steps?
Thank you for your assistance.
Best regards,
Nima Taghizadeh Mortezaei, M.D.
Radiation Oncology Research Fellow, MGH

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[Freesurfer] Issue with Voxel Size Mismatch in Samseg-Long Pipeline

[Taghizadeh Mortezaei, Nima]

Dear FreeSurfer Team,
I am working with two timepoints for a subject and attempting to create a 
template for samseg-long using mri_robust_template. However, I encountered an 
error related to voxel size mismatch between the input images. Both timepoint 
images are T1W.
The command I ran is:

mri_robust_template --mov subject1_preRT.nii subject1_postRT.nii --template 
mean.mgz --satit --mapmov subject1_preRT_reg.mgz
subject1_postRT_reg.mgz


I received the following error:

ERROR: MultiRegistration::loadMovables: images have different voxel sizes.
  Currently not supported, maybe first make conform?
  Debug info: size(1) = 0.428571, 0.428571, 4.4   size(0) = 0.449219, 0.449219, 
5
error: Operation not permitted
error: MultiRegistration::loadMovables: voxel size is different 
subject1_postRT.nii.


>From what I understand, mri_robust_template does not support different voxel 
>sizes between input images. Would the recommended approach be to first 
>resample the images to the same voxel size using mri_convert --conform or 
>another method before running mri_robust_template?
Additionally, would this resampling introduce any potential biases that I 
should be aware of in a longitudinal analysis? If there is a better way to 
handle this issue, I would greatly appreciate your guidance.
Best regards,
Nima

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Re: [Freesurfer] Inquiry About Longitudinal Analysis Using recon-all-clinical.sh

[Taghizadeh Mortezaei, Nima]

I appreciate any guidance or recommendations for my question.



From: Taghizadeh Mortezaei, Nima
Sent: Tuesday, February 11, 2025 9:45:25 AM
To: Freesurfer support list 
Subject: Inquiry About Longitudinal Analysis Using recon-all-clinical.sh

Dear FreeSurfer Community,

I want to work on a longitudinal analysis with two time points (pre-treatment 
and post-treatment) and would like to follow the recommended longitudinal 
pipeline. However, I want to use recon-all-clinical.sh and I want to ask 
whether the commands and steps for recon-all-clinical.sh are the same as the 
standard recon-all longitudinal pipeline? Are there any modifications or 
additional considerations required when using this script for longitudinal 
processing?

I appreciate any guidance or documentation references that could help with this 
analysis.

Thank you for your time and support!

Nima

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[Freesurfer] CSF Volume difference between recon-all-clinical and SAMSEG

[Taghizadeh Mortezaei, Nima]

Dear FreeSurfer Developers,

I seek clarification regarding a discrepancy in cerebrospinal fluid (CSF) 
volume measurements obtained using different FreeSurfer tools.

In my analysis, I measured CSF volume using both recon-all-clinical.sh and 
SAMSEG for the same subject. However, the results were significantly different:

recon-all-clinical: 236,073.36 mm³ (~236 mL)
SAMSEG: 471,854.76 mm³ (~472 mL)
Additionally, I conducted SAMSEG on 10 neurologically healthy subjects, and in 
all cases, the CSF volume was at least twice the normal average CSF volume 
(~150 mL) reported in the literature.

I would appreciate any insights into the following questions:

Why is there such a large discrepancy between the two methods?
Which method provides a more reliable estimate of total CSF volume?
Why are the estimated CSF volumes significantly higher than the known 
physiological average?

Thank you for your time and assistance!

Best regards,
Nima

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