Re: [Freesurfer] consistency in recon-all parallel pipeline

[Horn, Mitchell Jacob]

This is all with ‘recon-all -parallel’

Thanks,
Mitch

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Friday, February 23, 2024 2:30 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline

Do you run ‘recon-all -parallel’ or ‘recon-all –threads ’?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Horn, Mitchell Jacob
Sent: Friday, February 23, 2024 12:28 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline

Bottom line is that when I run any FreeSurfer version 7+ in parallel on COS8 I 
get different results each time.

Thanks,
Mitch

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Douglas N. Greve
Sent: Friday, February 23, 2024 11:03 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline

So, is the bottom line that when you run 7.4.1 on COS8 in parallel that you get 
(slightly) different results each time?
On 2/2/2024 11:20 AM, Horn, Mitchell Jacob wrote:

Hi FS Devs,



I’m experiencing unreproducible thickness results when running any 7+ version 
with parallelization enabled. Running recon-all without parallelization 
produces consistent thickness results. I’m running this in AlmaLinux8 (a 
library-equivalent downstream OS to CentOS8).



I’m attaching a table (table1) of 12 recons with bert:

  1.  3 parallelized with CentOS8-compiled 7.4.1
  2.  3 non-parallelized with CentOS8-compiled 7.4.1
  3.  3 parallelized with CentOS7-compiled 7.4.1
  4.  3 non-parallelized with CentOS7-compiled 7.4.1



I suspected the downstream CentOS8 libm was the culprit (because of testing I 
did this last 2023 summer). I ran 3 more recons parallelized with the 
CentOS7-compiled 7.4.1, but before running the recon-all command, set 
LD_PRELOAD to a copy of the CentOS7 libm libraries. The thickness results were 
then consistent, see the second table below (table2). I could not run this 
experiment on the CentOS8-compiled version, as that one is obviously not 
backward compatible with CentOS7 libm.



As a quick test of the OS-dependency, I submitted 3 parallel recons on MLSC 
with 7.3.3. Each reported different thickness. See table 3 (table3).



I’m asking if you can please confirm whether running any 7.+ version with 
parallelization is generating reproducible results for you in CentOS8 (or 
equivalent)?



P.S. - I tested 6.0 (CentOS6-compilation) with parallelization, and the results 
were consistent.

Best,
Mitch



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Re: [Freesurfer] consistency in recon-all parallel pipeline

[Huang, Yujing]

Do you run ‘recon-all -parallel’ or ‘recon-all –threads ’?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Horn, Mitchell Jacob
Sent: Friday, February 23, 2024 12:28 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline

Bottom line is that when I run any FreeSurfer version 7+ in parallel on COS8 I 
get different results each time.

Thanks,
Mitch

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Douglas N. Greve
Sent: Friday, February 23, 2024 11:03 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline

So, is the bottom line that when you run 7.4.1 on COS8 in parallel that you get 
(slightly) different results each time?
On 2/2/2024 11:20 AM, Horn, Mitchell Jacob wrote:

Hi FS Devs,



I’m experiencing unreproducible thickness results when running any 7+ version 
with parallelization enabled. Running recon-all without parallelization 
produces consistent thickness results. I’m running this in AlmaLinux8 (a 
library-equivalent downstream OS to CentOS8).



I’m attaching a table (table1) of 12 recons with bert:

  1.  3 parallelized with CentOS8-compiled 7.4.1
  2.  3 non-parallelized with CentOS8-compiled 7.4.1
  3.  3 parallelized with CentOS7-compiled 7.4.1
  4.  3 non-parallelized with CentOS7-compiled 7.4.1



I suspected the downstream CentOS8 libm was the culprit (because of testing I 
did this last 2023 summer). I ran 3 more recons parallelized with the 
CentOS7-compiled 7.4.1, but before running the recon-all command, set 
LD_PRELOAD to a copy of the CentOS7 libm libraries. The thickness results were 
then consistent, see the second table below (table2). I could not run this 
experiment on the CentOS8-compiled version, as that one is obviously not 
backward compatible with CentOS7 libm.



As a quick test of the OS-dependency, I submitted 3 parallel recons on MLSC 
with 7.3.3. Each reported different thickness. See table 3 (table3).



I’m asking if you can please confirm whether running any 7.+ version with 
parallelization is generating reproducible results for you in CentOS8 (or 
equivalent)?



P.S. - I tested 6.0 (CentOS6-compilation) with parallelization, and the results 
were consistent.

Best,
Mitch



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Re: [Freesurfer] Temporal lobe mask

[Douglas N. Greve]

you can run recon-all on the mni152 to get the aparc+aseg.mgz, then take 
the temporal lobe from that


On 2/23/2024 11:29 AM, Camargo, Aldo wrote:


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Hi there,

I would like to know where I can find a mask in MNI space for the 
temporal lobe.


Thanks a lot in advance for your help,

Aldo Camargo


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Re: [Freesurfer] overlay activation map on flattened surface

[Douglas N. Greve]

Just sample the activation onto the full surface (eg, --surf white 
--projfrac 0.5), then just load it as an overlay when you view the patch 
in freeview


On 2/22/2024 12:18 PM, Atena Akbari wrote:


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Hello Freesurfer team,

I have flattened the occipital patch using "mris_flatten -w 10 
subj04/surf/lh.occip.patch.3d subj04/surf/lh.occip.flattened" and it 
worked without any error and I can load the flattened patch in 
freeview. However, I have difficulty overlaying the activation map 
onto the flattened surface. Is the following command correct for this 
purpose?
(mri_vol2surf --mov   spmT_0001.nii --out  
subj04/surf/lh.bold.flat.mgz  --reg  fsl_reg.dat.lta   --surf 
occip.flattened  --hemi  lh)


Many thanks,

Atena


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Re: [Freesurfer] creating a cortical label using a 3D image ROI and calculating its volume and average thickness

[Douglas N. Greve]

You can run mri_vol2surf to sample the ROI onto the surface, eg,
mri_vol2surf --regheader subject --mov yourROI.mgz --projfrac-max 0 1 .1 
--hemi lh --o lh.yourROI.mgz

yourROI.mgz should be voxel-for-voxel aligned with the orig.mgz
View your sample with
tksurferfv subject lh inflated -aparc -ov lh.yourROI.mgz -fminmax 0.5 1
You can then get the thickness, area, vol with something like
mri_segstats --i lh.thickness --seg lh.yourROI.mgz --id 1 --sum 
summary.thickness.dat
When applying it to the area or volume files, make sure to add 
--accumulate to the command line



On 2/22/2024 8:24 AM, Yakupov, Renat /DZNE wrote:


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Dear Freesurfer users,


I would like to do the following:

- there is an ROI mask image file in the same space as the T1-weighted 
image


- I would like to use that mask to define the borders of a cortical area

- and then calculate volume and average thickness of the above defined 
cortical area



I know that I can get a rough estimate of the volume by applying the 
ROI mask to the the aparc* file and calculating the number of voxels, 
but what I would really like to do is use the ROI mask to constrain 
the WM and pial surfaces to the volume inside the ROI and then 
calculate statistics using the surfaces approach.



I also know that I can combine existing labels, but unfortunately this 
custom ROI contains parts of various cortical regions, not whole regions.



Any advice would be appreciated!


Best wishes,

Renat.


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Re: [Freesurfer] Creating a custom registration template with FreeSurfer template

[Douglas N. Greve]

Can you include the full terminal output for one of the mris_preproc 
commands that is failing?


On 2/22/2024 7:12 AM, Asuka Toyofuku wrote:


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Dear Freesurfer experts,


I have issues with creating a custom registration template. (I'm 
following this instruction: *MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates 
 )



According to the instructions, we need to

1) Create an average subject (Creates $SUBJECTS_DIR/newtemplate)

2) Register each subject to the new template (do for both lh and rh), 
resulting in lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate

3) Get thickness values in the newtemplate space for GLM analysis
4) Create another average template based on the previous one: (Creates 
$SUBJECTS_DIR/newnewtemplate)


I'm stuck with the 3) command.
Instruction suggests:
mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s 
subj3 ...


and this is my code:
for d in Teen*
do mris_preproc --surfreg sphere.reg.teenheart_average_template --s $d 
--hemi lh --out lh.surfreg.teenheart_average_template.thickness --meas 
thickness

done

( I specified hemi and output because, without it, I got ERROR: no 
source hemi specified)


My command led to an error saying:

ERROR: format for lh.surfreg.teenheart_average_template.thickness not 
recognized


So my questions are:

a) what does it mean that "format for 
lh.surfreg.average_template.thickness not recognised"? Any ideas on 
how to fix this?


b) Does this mris_preproc --surfreg command produce different 
smoothing mgh files? (e.g., fwhm10, fwhm15, fwhm20...?)


Because standard mris_preproc before GLM analysis(*MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming 
to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis 
) 
are done with previously qcashed data (e.g., need 
thickness.fwhm10.fsaverage to run mris_preproc), but at this point, I 
don't have any of these thickness files with different smoothing levels.


c ) If this mris_preproc --surfreg command does not generate a set of 
thickness maps in **newtemplate space** at different smoothing levels, 
what kind of command should I run?



Any input is appreciated!


Best regards,

Asuka


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Re: [Freesurfer] How to write rh.w-g.pct from recon-all stats output into a table

[Douglas N. Greve]

Do you see a subject/stats/lh.w-g.pct.stats file?
You can use asegstats2table to compile this across subjects. Run it with 
-help to get more info


On 2/22/2024 3:26 AM, ERNEST KISSI wrote:


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I processed several items of data. And I have rh.w-g.pct file in my stats
folders.
How can I get process this file to get table reading file? I tried to use
asegstats2table and aparcstats2table but it didn’t work.
Could you provide me with necessary information about getting of stats 
from

rh.w-g.pct to table file like asegstats2table?
Thank you.

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Re: [Freesurfer] Using MRI_segstats to calculate grey matter intensity

[Douglas N. Greve]

Yes, you just have to make sure the input and seg volumes are in voxel 
for voxel alignment


On 2/21/2024 4:30 AM, ERNEST KISSI wrote:


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Hello freesurfer Team,

I have the grey matter segmentation from FSL and I have freesurfer 
recon-all output but the recon-all outputs do not have regional grey 
matter intensities. Can I use MRI_segstats to calculate the regional 
grey matter output using the FSL grey matter segmentation and the 
recon-all subject hemi parc and subject hemi labels to get the various 
brain parts and labels for the grey matter?


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Re: [Freesurfer] formula calculating percent signal change

[Douglas N. Greve]

In what context? For fMRI, it is the signal change divided by the signal 
mean (x100%)



On 2/20/2024 6:43 PM, Tina Zahrie wrote:


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Hi all,

How is the percent signal change calculated within a ROI? What is the 
formula for it?


Thanks,
Tina


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Re: [Freesurfer] psf formula PET SURFER

[Douglas N. Greve]

I'm not sure what you are looking for as it is just the equation of a 
gaussian. The PSF is given as the full-width-half-max. This is converted 
to a std dev with

gstd = fwhm/sqrt(log(256.0))


On 2/18/2024 7:03 AM, Federica Di Antonio wrote:


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Dear experts,

I'm employing PETsurfer for partial volume correction.
Could you share the definition or formula you use to define the psf 
(flag --psf of mri_gtmpvc) that is used to correct the PET image?
I understand that it is an isotropic gaussian filter, but could you 
maybe provide the precise formula you employ or the reference you 
refer to?


Thank you so much for your kindness and availability,

Federica Di Antonio


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Re: [Freesurfer] consistency in recon-all parallel pipeline

[Horn, Mitchell Jacob]

Bottom line is that when I run any FreeSurfer version 7+ in parallel on COS8 I 
get different results each time.

Thanks,
Mitch

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Friday, February 23, 2024 11:03 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline

So, is the bottom line that when you run 7.4.1 on COS8 in parallel that you get 
(slightly) different results each time?
On 2/2/2024 11:20 AM, Horn, Mitchell Jacob wrote:

Hi FS Devs,



I’m experiencing unreproducible thickness results when running any 7+ version 
with parallelization enabled. Running recon-all without parallelization 
produces consistent thickness results. I’m running this in AlmaLinux8 (a 
library-equivalent downstream OS to CentOS8).



I’m attaching a table (table1) of 12 recons with bert:

  1.  3 parallelized with CentOS8-compiled 7.4.1
  2.  3 non-parallelized with CentOS8-compiled 7.4.1
  3.  3 parallelized with CentOS7-compiled 7.4.1
  4.  3 non-parallelized with CentOS7-compiled 7.4.1



I suspected the downstream CentOS8 libm was the culprit (because of testing I 
did this last 2023 summer). I ran 3 more recons parallelized with the 
CentOS7-compiled 7.4.1, but before running the recon-all command, set 
LD_PRELOAD to a copy of the CentOS7 libm libraries. The thickness results were 
then consistent, see the second table below (table2). I could not run this 
experiment on the CentOS8-compiled version, as that one is obviously not 
backward compatible with CentOS7 libm.



As a quick test of the OS-dependency, I submitted 3 parallel recons on MLSC 
with 7.3.3. Each reported different thickness. See table 3 (table3).



I’m asking if you can please confirm whether running any 7.+ version with 
parallelization is generating reproducible results for you in CentOS8 (or 
equivalent)?



P.S. - I tested 6.0 (CentOS6-compilation) with parallelization, and the results 
were consistent.

Best,
Mitch




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[Freesurfer] ERROR: awk -f in Talairach registration and multibyte conversion failure; possibly due to region settings?

[Mohn, Johannes Julius]

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Dear Freesurfer Developers,


I installed Freesurfer 6.0.0 fresh on a Macbook Pro (2021) with M1 chip running 
macOS Monterey 12.5.


I tried to run recon-all on both on the bert data shipped with freesurfer and 
my own brain data in .nii.gz format (standard T1 sequence). Both process start 
fine but abort at the exact same step with an error in Talairach registration.


The command I use is:

$> recon-all -i sub-20190911.nii.gz -s jjm -all

SUBJECTS_DIR is set correctly; sub-20190911 exists.

I receive the following error:


ERROR: awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk 
/Users/jjm/sci/freesurfer_data/bert/mri/transforms/talairach_avi.log failed!


The contents of the talairach_avi.log are as follows:


awk: towc: multibyte conversion failure on: ' '

input record number 86, file 
/Users/jjm/freesurfer_data/jjm/mri/transforms/talairach_avi.log
source line number 8


For better diagnostics, I'm attaching the recon-all.log and talairach_avi.log 
and avi_QA.log. Interestingly, in previous attempts to run recon-all, I had 
received the same error with multibyte conversion failure on 'Ù' and later on 
'ö'. I suspected that at some level this is related to language and region 
settings on my machine. Therefore, I changed region from Germany to United 
Kingdom and keyboard from German QWERTZ to US keyboard layout (language has 
always been English on my machine). As a result the reported error regarding 
multibyte conversion changed from 'Ù' / 'ö' to now ' ', but the error 
stubbornly persists. Are there any known issues with running Freesurfer on 
particular region/language/keyboard settings?


Thank you in advance for help in debugging this.


Best regards,
JJ



__


Johannes Julius Mohn

Doctoral candidate
Max Planck School of 
Cognition


Institut für Medizinische Psychologie

Charité – Universitätsmedizin Berlin


Campus Charité Mitte | Luisenstr. 57 | 10117 Berlin

T +49 030 450 529 213

johannes.m...@charite.de

http://secure-web.cisco.com/1Fmh9RNa1Lp2C3p3fMNDLavMb1aZuOMd8wv3n950I6oYSLtRBdJZEvkavCiKqVO5sU-zASOMJ_bHOxjS2irsp49WnCGNP8iwm66GWKTzivHFPNnhX1XVRDe_yJS-cO1Q7sgK-i_FAIg9MKnOCOWSAIK12l1frtQ7NqOvTikMyzQ2tTB3VaNUXGsOncpHGEMkeBVP58ab37sQNFlloDZIecEb_YqslG44bvtTcC0-5NE_I2O3oB_Pc0ybY079rvxhlj4WwUxh4yf1nhvHwEKh7XmkUU4jXRiThRBReZmuh_FwY3uFgtnRuJIQhD-8PWH1m8tR0zcdGjdmWZqCBNo3ZRg/http%3A%2F%2Fwww.charite.de


recon-all.log
Description: recon-all.log


talairach_avi.log
Description: talairach_avi.log


talairach_avi_QA.log
Description: talairach_avi_QA.log
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Re: [Freesurfer] if: Expression Syntax - preproc-sess

[Douglas N. Greve]

I cannot reproduce this locally. If you still want help, attach logs. 
You can also try running it with -debug as the first option and capture 
the copious terminal output.


On 2/6/2024 8:39 AM, Huang, Yujing wrote:


Not sure where this happened. Does it produce any log files that you 
can share? Maybe both logs with and without the -nomc option.


Best,

Yujing

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Stefano Delli 
Pizzi

*Sent:* Saturday, February 3, 2024 2:33 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] if: Expression Syntax - preproc-sess

*External Email - Use Caution *

Hello FreeSurfer Developers,
I'm attempting to run preproc-sess with -nomc option
preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 
-fsd rest

-per-run -sliceorder up -force
if: Expression Syntax.
This error occurred before to create the file with slice timing correction
The error did not occur when I run the preproc-sess command line 
without the

-nomc option.
I've searched the list and no similar errors have been reported. Does 
anyone

have any thoughts on how to trouble-shoot this one?
FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
Platform: Darwin Kernel Version 21.6.0

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[Freesurfer] Temporal lobe mask

[Camargo, Aldo]

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Hi there,

I would like to know where I can find a mask in MNI space for the temporal lobe.

Thanks a lot in advance for your help,

Aldo Camargo

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Re: [Freesurfer] Fwd: Vertex / voxel lesion symptom mapping

[Douglas N. Greve]

Sorry, don't know what VLSM is. Can you elaborate?

On 2/6/2024 3:19 PM, Martin Juneja wrote:


External Email - Use Caution

Dear FreeSurfer community and experts,

I would greatly appreciate any help/response with the following.

Thanks.

-- Forwarded message -
From: *Martin Juneja* 
Date: Wed, Jan 31, 2024 at 7:51 PM
Subject: Vertex / voxel lesion symptom mapping
To: Freesurfer support list 


Greetings FreeSurfer community,

I was just wondering if it's possible to perform vertex/voxel lesion 
symptom mapping (VLSM) using FreeSurfer? In other words, I would like 
to assess the impact of lesion topography (of course, heterogenous 
locations across patients) on neurocognitive function in brain tumor 
patients.


I would greatly appreciate any help/response.

Thanks!

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Re: [Freesurfer] aseg QA questions

[Douglas N. Greve]

On 2/6/2024 2:01 PM, Sarah Skinner wrote:


External Email - Use Caution

Question 1 - We found a few voxels that are labeled as the right 
choroid-plexus, but it is nowhere near the rest of the structure. See 
attached image. Is this a problem? If yes, what is the best way to fix 
this?

Probably not a problem as it is just a few voxels.


Question 2 - The right-lateral-ventricle appears to be separated into 
2 unconnected areas. We are assuming this is okay, but we wanted a 
second opinion. See attached image.
Yes, this is ok and often happens in younger subjects where the channel 
between the two areas is very narrow.


Thanks!

Sarah Skinner
Research Specialist
Institute on Aging
University of Wisconsin-Madison

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Re: [Freesurfer] Cortical WM parcellation for DKT atlas?

[Douglas N. Greve]

If  you look in the recon-all.log file (or recon-all.cmd file), you will 
find the command that creates the wmparc.mgz. You can adapt it to use 
the DKT


On 2/6/2024 6:53 AM, Hamied Haroon wrote:


External Email - Use Caution

Hello Freesurfer Gurus,

Is it possible to obtain “wmparc” but for the DKT cortical atlas, please?

Many thanks.

Best wishes,

Hamied

*Dr Hamied A Haroon*[he/him/his], MSc, PhD, MInstP

Research Fellow in Quantitative Biomedical MR Imaging

The University of Manchester


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Re: [Freesurfer] Manual/reproduce conform

[Douglas N. Greve]

The TkR vox2ras will never have direction cosine info. The -conform-dc 
will keep the original DC in the "conformed" volume (eg, orig.mgz vs 
rawavg.mgz)


On 1/11/2024 3:22 PM, Dipterix Wang wrote:


External Email - Use Caution

I tried `--conform-dc` and the flag was not recognized. `-conform-dc` 
didn't give me error. However, vox2ras-tkr still didn't include the 
cosine information.


This is the Torig:

mri_info --vox2ras-tkr T1.mgz

-1.0    0.0    0.0  128.0

0.0    0.0    1.0 -128.0

0.0   -1.0    0.0  128.0

0.0    0.0    0.0    1.0


While Norig is

mri_info --vox2ras T1.mgz

-0.99989    0.00604    0.01331  124.66034

0.01408    0.15990    0.98703 -164.17455

-0.00383   -0.98711    0.15997  108.14072

0.0    0.0    0.0    1.0


I wonder what steps I could take to make sure the Torig = Norig. Here 
Norig is acpc realigned.


Best,
- D

On Mon, Jan 1, 2024 at 4:27 PM Douglas N. Greve 
 wrote:


If you want to keep the original orientation, you can specify
--conform-dc. Would that fix your problem?

On 12/21/2023 9:30 AM, Dipterix Wang wrote:


External Email - Use Caution

Dear FreeSurer Wizards,

I'm trying to run the recon-all command on one of my template
brains such that the resulting Norig and Torig are identical. I
understand that fs always conforms the MRI to 256^3 before
segmentation. I wonder if there is any way that I can resample
the original MRI to achieve the same Norig and Torig?

More specifically, currently the Torig (vox to tkrRAS) is
     [,1] [,2] [,3] [,4]
[1,]   -1    0    0  128
[2,]    0    0    1 -128
[3,]    0   -1    0  128
[4,]    0    0    0    1

If I resample the input image such that Norig (vox to scanRAS)
equals this matrix, can I expect that "conform" does not change
the orientation?

Alternatively, is there any method I can use to "predict" or
reproduce the Torig from the original MRI outside of FreeSurfer?

Thanks,
- Dipterix


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>
.

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Re: [Freesurfer] Getting from MNI152 to fsaverage

[Douglas N. Greve]

Hi Lauri, that command does look right (and no need to worry about that 
warning). The projfrac is the projection fraction. This is the distance 
away from the white surface that fMRI will be sampled relative to the 
thickness at that location. So a value of 0.5 means to sample in the 
middle of the ribbon, which is probably where you want to sample. There 
are other options (eg, you can sampled a fixed mm distance).

doug


On 2/2/2024 1:15 PM, Lauri Tuominen wrote:


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Dear experts,

I am comparing freesurfer mri_vol2surf to nilearn surface.vol_to_surf. 
I am finding large differences so I just wanted to get this command 
absolutely right before making any sort of conclusions.



I would love if someone could confirm this is ok:


```

mri_vol2surf --mov task-rest_space-MNI152NLin6Asym.bold.nii.gz \

--mni152reg \

--hemi lh \

--surf white \

--o lh.task-rest_space-fsaverage.bold.nii.gz

```


Also I get complains about source volume voxel size (2,2,2) being 
different from target voxel size (1,1,1). I did read somewhere that 
this warning can be ignored. Is that correct?



fsfast pipeline seems to use default projection fraction 0.5, while 
the default in the above command is 0. Could someone explain me the 
reasoning behind this? I am wondering if I should be using 0.5 or 0 
with my data.



Thank you so much!!

Lauri






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Re: [Freesurfer] consistency in recon-all parallel pipeline

[Douglas N. Greve]

So, is the bottom line that when you run 7.4.1 on COS8 in parallel that 
you get (slightly) different results each time?


On 2/2/2024 11:20 AM, Horn, Mitchell Jacob wrote:


Hi FS Devs,

I’m experiencing unreproducible thickness results when running any 7+ 
version with parallelization enabled. Running recon-all without 
parallelization produces consistent thickness results. I’m running 
this in AlmaLinux8 (a library-equivalent downstream OS to CentOS8).


I’m attaching a table (table1) of 12 recons with bert:

  * 3 parallelized with CentOS8-compiled 7.4.1
  * 3 non-parallelized with CentOS8-compiled 7.4.1
  * 3 parallelized with CentOS7-compiled 7.4.1
  * 3 non-parallelized with CentOS7-compiled 7.4.1

I suspected the downstream CentOS8 libm was the culprit (because of 
testing I did this last 2023 summer). I ran 3 more recons parallelized 
with the CentOS7-compiled 7.4.1, but before running the recon-all 
command, set LD_PRELOAD to a copy of the CentOS7 libm libraries. The 
thickness results were then consistent, see the second table below 
(table2). I could not run this experiment on the CentOS8-compiled 
version, as that one is obviously not backward compatible with CentOS7 
libm.


As a quick test of the OS-dependency, I submitted 3 parallel recons on 
MLSC with 7.3.3. Each reported different thickness. See table 3 (table3).


I’m asking if you can please confirm whether running any 7.+ version 
with parallelization is generating reproducible results for you in 
CentOS8 (or equivalent)?


P.S. - I tested 6.0 (CentOS6-compilation) with parallelization, and 
the results were consistent.


Best,

Mitch


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Re: [Freesurfer] Freesurfer white matter overestimated

[Douglas N. Greve]

Hi, no snapshots were attached.

On 2/1/2024 6:02 AM, Luisa Klahn wrote:


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Hello!
I am processing structural data from a 3T scanner using Freesurfer 
version 7.3.2. For some subjects, the grey matter looks very thin, and 
the white matter looks overestimated. I'll attach screenshots of the 
brainmask, wm mask, and T1 including wm and pial surface lines.
I have tried to set control points into the wm but this did not change 
the results.


Does anyone have an idea? Would it be possible to change the intensity 
settings in the recon-all command?


Thanks for helping!
Luisa

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Re: [Freesurfer] Fixing intensity normalization issue which leads to gray matter classified as WM

[Douglas N. Greve]

Are you saying that synthseg itself is generating the wrong seg or that 
something is going wrong further downstream? The recon-all stream with 
synthseg is not a supported pipeline at the moment. For the standard 
stream, can you send the full recon-all.log file?


On 1/29/2024 2:04 PM, Maya Yablonski wrote:


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Hello,

I am running freesurfer v7.3.2 reconall with -synthseg on a pediatric 
sample, and for one specific subject I keep getting a lot of gray 
matter classified as white matter, which leads to the ?h.white 
surfaces being too close to the pial surface. I have tried running 
with and without the --robust option but the issue recurs. Are there 
any expert options that I can play with before manually editing the 
WM.mgz? The issue is pervasive throughout the brain so will require 
heavily editing every single slice. The values for the misclassified 
gray matter are 85-97 in the brainmask.mgz and 100-110 in the WM.mgz 
and the T1 image looks ok by eye. When trying to run the same subject 
with the default pipeline (no synthseg), it crashes with the following 
error:


reading 1 input volumes...
logging results to talairach.log
reading 
'/share/software/user/open/freesurfer/7.3.2/average/RB_all_2020-01-02.gca'...

GCAread took 0 minutes and 1 seconds.
average std = 7.2   using min determinant for regularization = 5.2
0 singular and 884 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
error: mghRead(/MYPATH/freesurfer/sub-2341/mri/brainmask.mgz, -1): 
could not open file

error: mri_em_register: could not open mask volume brainmask.mgz.

I wonder if there's any parameter I can tweak in the expert.opts?
Thanks for any leads,
Maya

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