Re: [Freesurfer] recon-all process still not finishing properly

[Douglas N. Greve]

not sure what is happening. You can run recon-all with -debug and 
capture the output (both stdout and stderr) into a file. This will cause 
it to print out huge amounts of text specifying what it is doing on each 
line. You should also see if there is some stderr output that is not 
being caught. You can try running recon-all -fill on the subject that 
you created to see if the fill will run at all (this may be easier than 
waiting 4 hours).


On 4/8/2024 3:18 PM, Dong, Yilei wrote:


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Hi Freesurfer Support,

The past few weeks, I've emailed about my recon-all processing stream 
never completely finishing.
We are still encountering the same problem. For context, our recon-all 
job submission script runs recon-all for 1 image. Given a folder of 
100 MRI images, we have another script that calls upon the recon-all 
script for each image within the folder via a for loop. The result is 
100 jobs running in parallel on the cluster.


I have attached a screenshot of the parameters we set whenever we 
submit each recon-all job for each image by SLURM to UCSD's cluster. 
The maximum time we are allowed for each job is 48 hours. Our jobs are 
shared-node jobs, which means we run more than 1 job on a single node. 
This time, we increased RAM from 8GB to 16GB in hopes the entire 
recon-all processing stream can fully run through for each image, but 
it still stops at "mri_pretess done" and does not go on to the -fill 
step. Each job submitted to the cluster took around 4 hours and 20 
minutes each to run in our most recent attempt.


If increasing the RAM did not change anything for us, how else can we 
get more verbose error messages? What other reasons could be why our 
recon-all aborts before finishing? I have attached a recon-all.log 
from one of our subjects for reference and a screenshot of the 
parameters we set for submitting jobs in our cluster for reference.



Freesurfer version: 7.2.0, but already available as module on UCSD's 
cluster system


Platform: Rocky Linux release 8.8 (Green Obsidian)

uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 
15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux


Recon-all log: see attached


Thank you!


Sincerely,

Yilei


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Re: [Freesurfer] Enorm threshold for dynamic PET images

[Douglas N. Greve]

Sorry, I don't know what you mean by enorm threshold. Can you elaborate?

On 4/4/2024 4:39 PM, Sneha Pandya wrote:


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Dear team,

I am using mc-afni2 to perform motion correction on dynamic PET images 
(ref: petsurfer wiki page). I am planning to use an average of 
un-censored frames as a template to do so. What should the threshold 
be to estimate these set of un-censored frames? For fMRI we usually 
use 0.2 or 0.3 for motion. However, for PET data we have values in the 
enorm file ranges from 0-40.


Thank you,

Sneha


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Re: [Freesurfer] GLM Using 2 Surfaces - Thickness and Area

[Douglas N. Greve]

On 4/18/2024 1:59 PM, Tejaswi D. Sudhakar wrote:


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Hello Freesurfer team,

I am interested in doing one glm analysis using both the thickness and 
cortical surface area.


My question is two-fold:

First, is it possible to provide both the thickness and area files to 
mris_preproc and mri_surf2surf commands or is it only possible to run 
two separate glms (one for thickness and one for area)?



You must run two separate glms


Second, can we consider thickness and area as separate values or are 
they both correlated? In other words, how correlated are the thickness 
and area values?


They should be uncorrelated by construction (ie, the noise in the 
thickness should be uncorrelated from that in the area), but they may 
biologically correlated (don't know). When doing an area analysis, make 
sure to turn on jacobian correction (on by default when you spec area to 
mris_preproc) and correct for total head size. You will also need to do 
the permutation corrections for multiple comparisons (for both thickness 
and area but esp for area).


Thanks in advances,

Tejaswi


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Re: [Freesurfer] gunzip error in load_mgh.m when file path contains spaces

[Douglas N. Greve]

thanks, just checked in your change.

On 4/17/2024 9:37 PM, Tyler Slouf wrote:


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Hello FreeSurfer Developers,

I found what I believe to be a bug. Typically I can load mgz files 
into my Matlab program without any trouble.

But if the path containing the mgz file has a space then I get an error.

When I run this very short script in Matlab calling the MRIread 
function (/Applications/freesurfer/7.4.1/matlab/MRIread.m):


filepath = char("/Users/user/Documents/folder space test/data/mri.mgz");
mri = MRIread(filepath);

I get the following error:

gunzip: can't stat: /Users/user/Documents/folder 
(/Users/user/Documents/folder.gz): No such file or directory

gunzip: can't stat: space (space.gz): No such file or directory
gunzip: can't stat: test/data/mri.mgz (test/data/mri.mgz.gz): No such 
file or directory


ERROR: problem reading fname
SWITCH expression must be a scalar or a character vector.

Error in load_mgh (line 163)
switch type

Error in MRIread (line 90)
[mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);

Error in test_load_mgz (line 2)
mri = MRIread(filepath);

I traced this down to the function *load_mgh.m 
(*/Applications/freesurfer/7.4.1/matlab/load_mgh.m) where a file path 
string
(char array) is dynamically populated with randomly generated folder 
names to unzip into.

It's about line 69 and looks like this:
[status,msg] = unix(sprintf('gunzip -c %s > %s', fname, new_fname));

You may notice that potential spaces in the path names fname and 
new_fname are not escaped with single quotes.

I edited the file to escape the parameterized strings like so:
[status,msg] = unix(sprintf("gunzip -c '%s' > '%s'", fname, new_fname));

This solved the problem for me.

Computer details:
OS: MacOS Sonoma (latest)
Chipset: Apple M1 (aarch64)
Calling Program: Matlab R2023b
Freesurfer: 7.4.1

Thank you for your time.

Sincerely,
Tyler Slouf

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Re: [Freesurfer] Skin-Skull-Brain segmentation

[Douglas N. Greve]

You can try running samseg. This will generate most of the layers you 
want, but in segmentations. You will have to convert them to surfaces 
(eg, mri_tesssellate or mri_binarize with --surf output)


On 4/15/2024 5:31 AM, XIE Jing wrote:


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Hello all,

We would like to use FreeSurfer to remodel the head, not only 
including the detailed brain structural information, but also 
considering skin and skull. I am wondering if the FreeSurfer is 
possible to split the skin, skull and brain surfaces at the same time?


We tried the syntax "mri_make_bem_surfaces -all" , and the error notes 
were received as follows:

/nvertices=2562, nfaces=5120 /
/mri_strip_skull: triangle file 
/home/customer/Desktop/headmodel/FREESURFER/freesurfer/lib/bem/ic4.tri 
read trishrink: File 
/home/customer/Desktop/headmodel/MRI/-all/mri/brain/COR-.info not found /

/Best guess at inner_skull.tri is in inner_skull_tmp.tri/

What's your suggestions and comments on this question? We appreciate 
it very much!


Thanks in advance!
Jing
*---*
*Jing XIE*
Associate Professor
Mechatronical Engineering
Beijing Institute of Technology
Beijing 180001, PR China


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Re: [Freesurfer] surface-based filtering

[Douglas N. Greve]

Yes, you can also run
mris_fwhm --smooth-only --i input.surf-values.mgz --fwhm FWHM --s 
subject --hemi hemi --o output.surf-values-smoothed.mgz --cortex

This will give the same result as mri_surf2surf

On 4/12/2024 10:07 PM, Jiaen Liu wrote:


External Email - Use Caution

I found in the source code about the use of fwhm. It decides the 
number of iterations to achieve a gaussian filter with the specified 
fwhm in mm


Best,
Jiaen
Sent with my mobile device

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Jiaen Liu 


*Sent:* Thursday, April 11, 2024 3:58:18 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

External Email - Use Caution

I thought N controls the number of smoothing iterations and the 
smoothing in each iteration is defined by fwhm which is some 
measurement of the smoothing kernel width.


Can I ask how to achieve smoothing effect similar to gaussian 
smoothing with certain sigma, where sigma is defined by voxel unit?


Thanks!

Best

Jiaen

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Fischl, Bruce 
R.,PHD

*Sent:* Thursday, April 11, 2024 15:50
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

Hi Jiaen

I’m not sure what you mean by “stacked smoothing”. I think the N in 
nsmooth is the number of iterations of nearest neighbor smoothing to 
apply, which  converges to Gaussian as N gets bigger. Not sure about 
the units for fwhm – I defer to Doug on that


Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Jiaen Liu

*Sent:* Thursday, April 11, 2024 4:41 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

*External Email - Use Caution *

Hi Bruce

Thanks for your response. In the help, I found the following options. 
Is the fwhm based on voxel unit? Does nsmooth-in or-out control the 
number of stacked smoothing?


--fwhm-src fwhmsrc: smooth the source to fwhmsrc

--fwhm-trg fwhmtrg: smooth the target to fwhmtrg

--nsmooth-in N  : smooth the input

--nsmooth-out N : smooth the output

Best

Jiaen

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Fischl, Bruce 
R.,PHD

*Sent:* Thursday, April 11, 2024 14:24
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

*EXTERNAL MAIL*

Yes, we support surface-based smoothing. Check out the help for 
mri_surf2surf


Cheers

Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Jiaen Liu

*Sent:* Thursday, April 11, 2024 2:14 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] surface-based filtering

*External Email - Use Caution *

I’m wondering if freesurfer provides functions to filter the surface 
data within certain neighborhood exclusively on the surface. It’s 
essentially similar to regular smoothing in 3D space. But the 
filtering kernel only runs on the surface.


I can think of a solution to filter adjacent vertex in the surface 
file. But I’m not sure if the adjacent vertex is also close in space.


Thanks!

Best regards,

*Jiaen Liu Ph.D.*

Assistant Professor

*/Advanced Imaging Research Center & Radiology/*

UT Southwestern Medical Center

2201 Inwood Ln

Dallas, TX, USA, 75390

Office: 214.645.2750

Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, Texas 

Re: [Freesurfer] BBRegistration with FSL topup

[Douglas N. Greve]

The vsm (voxel shift map) needs to be in the same voxel space as the 
fMRI (ie, it has to have the same voxel size, number of voxels, and the 
voxels must line up with the fMRI)


On 4/11/2024 8:11 PM, Gianluca Guglietti wrote:


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Hi,

I had a question as to how to integrate fsl's topup command for 
correcting B0 distortion with freesurfer's boundary-based 
registration. I am working with high-resolution epi data (0.8mm 
isotropic) with a reduced FOV and am trying to register it to an 
MP2RAGE structural scan that I've already run through free surfer's 
recon-all. When I use the BBR command it works perfectly fine but when 
I try to add the topup field map it fails, returning this error 
"MRIvol2surfVSM: vsm dimension mismatch 1".


the field map was generated using two reverse phase encoded SE-EPI 
volumes with the same resolution and field of view as the GE-EPI BOLD 
data I am trying to register.


Any advice would be greatly appreciated!

Best,

Gianluca

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Re: [Freesurfer] question about infantfreesurfer

[Zollei, Lilla,Ph.D.]

Hi Knut,
Can you clarify what you mean by your question?
Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Knut J Bjuland 

Sent: Friday, April 5, 2024 2:38 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] question about infantfreesurfer


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Dear freesufer experts,
 Does anyone know whether infantFreesurfer is ready to use for publication 
purposes? Thank you! Knut Jørgen Bjuland, PhD Telemark Hospital
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Re: [Freesurfer] Default intensity values for gray and white matter

[Fischl, Bruce R.,PHD]

Hi Sanna

They were kind of hand tuned ages ago, but I'm pretty sure that they get 
re-estimated by a procedure that adapts to the intensities in the input images. 
They were probably tuned for a specific class of T1-weighted scans (like 
FLASH), but the adaptive estimation usually works well on a broad variety of 
scans (like MP-RAGE, where you trade off higher noise for better contrast)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Lokhandwala, Sanna
Sent: Thursday, April 18, 2024 1:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Default intensity values for gray and white matter


External Email - Use Caution
Dear FreeSurfer developers,


I am interested in understanding where the freesurfer default intensity values 
for gray and white matter specifically come from within the recon-all command. 
I understand the default intensity of white matter (mean) is 110, white matter 
(low) is 90, white matter (high) is 125, gray matter (low) is 30, and gray 
matter (high) is 100. I know that the default parameters are meant to improve 
segmentation of the gray and white matter tissue but could you please tell me 
how/where these values come from? I've read the 2002 paper "Whole Brain 
Segmentation: Automated Labeling of Neuroanatomical Structures in the Human 
Brain" and I saw that Figure 1 had varying distributions for gray and white 
matter intensity, but I did not see anything that explicitly stated how these 
default values were chosen.

Your guidance is appreciated,
Sanna Lokhandwala
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[Freesurfer] GLM Using 2 Surfaces - Thickness and Area

[Tejaswi D. Sudhakar]

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Hello Freesurfer team,

I am interested in doing one glm analysis using both the thickness and cortical 
surface area.

My question is two-fold:

First, is it possible to provide both the thickness and area files to 
mris_preproc and mri_surf2surf commands or is it only possible to run two 
separate glms (one for thickness and one for area)?

Second, can we consider thickness and area as separate values or are they both 
correlated? In other words, how correlated are the thickness and area values?

Thanks in advances,
Tejaswi

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[Freesurfer] Default intensity values for gray and white matter

[Lokhandwala, Sanna]

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Dear FreeSurfer developers,

I am interested in understanding where the freesurfer default intensity values 
for gray and white matter specifically come from within the recon-all command. 
I understand the default intensity of white matter (mean) is 110, white matter 
(low) is 90, white matter (high) is 125, gray matter (low) is 30, and gray 
matter (high) is 100. I know that the default parameters are meant to improve 
segmentation of the gray and white matter tissue but could you please tell me 
how/where these values come from? I’ve read the 2002 paper “Whole Brain 
Segmentation: Automated Labeling of Neuroanatomical Structures in the Human 
Brain” and I saw that Figure 1 had varying distributions for gray and white 
matter intensity, but I did not see anything that explicitly stated how these 
default values were chosen.

Your guidance is appreciated,
Sanna Lokhandwala
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Re: [Freesurfer] vertices are -1 when using vol2label

[Douglas N. Greve]

vertices require a surface. There is no surface for cerebellum, so the 
vertices are all marked -1 to indicate that the vertex indices are not 
valid. The XYZ values are valid though


On 4/9/2024 6:36 AM, Sam W wrote:


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Hello!
I'm trying to convert the cerebellum cortex in the aparc+aseg.mgz into 
a label so I tried:


mri_vol2label --c bert/mri/aparc+aseg.mgz --id 8 --l lh.cerebellum.label

but the resulting output file only has -1 as vertices. Is there 
anything wrong with the command above?


Best regards,
Sam

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