[Freesurfer] Synthsr command !

[Martin Juneja]

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Dear Juan and FreeSurfer developers,

I am trying to run the *mri_synthsr *command on a MacPro M2 Max chip (OS
13.6.4) - but somehow, I am getting the following error when I try to run
this command. I am using FreeSurfer's 7.4.1 version.

*Illegal instruction: 4*


I would greatly appreciate any help in getting this resolved.



Thanks.
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[Freesurfer] [TRACULA] how to setup with opposite phase-encoding

[Fahad Hannan]

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Hi,

I've been trying to use TRACULA on my data, trying to setup a configuration 
file but I am having some difficulty on how to incorporate my data.

I have a DWI scan with 65 volumes (1 b0 image, 64 with b = 1000)
I also have separate volumes for b0 pairs having opposite phase-encoding 
directions.

I am not sure how to incorporate these into the configuration file. I can do it 
with using just the one b0 image, but I'd like to use the opposite 
phase-encoding as well.

How would I go about this in the configuration file?

Thanks,
Fahad Hannan
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Re: [Freesurfer] Calculation of MRI intensity

[Douglas N. Greve]

you will have to binarize it first, eg, mri_binarize --i inputimage.mgz 
--min threshold --o binary.mgz, then run mri_segstats --seg binary.mgz 
--id 1 --i inputimage.mgz --sum sum.dat


On 2/7/2024 8:55 AM, Huang, Yujing wrote:


I think mri_segstats –i option will do that - 
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats


Best,

Yujing

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *ERNEST KISSI

*Sent:* Wednesday, February 7, 2024 8:12 AM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] Calculation of MRI intensity

*External Email - Use Caution *

Hi Freesurfer Team,

Please I want to calculate the mean intensity of a skullstripped MRI 
image. I do not want to use recon-all because I do not want to 
parcellate or segment it. Is there such utility or function in freesurfer?


Thank you.

Sincerely,

Ernest Kissi Kontor.


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Re: [Freesurfer] No ROI name in summary of MNI305 group analysis

[Douglas N. Greve]

Try adding -seg fsaverage aparc+aseg.mgz


On 1/26/2024 4:59 AM, wangzhiwei3233 wrote:


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Dear Gouglas,
Thank you for your replay. There is still no ROI name in the summary 
after adding --reg $SUBJECTS_DIR/fsaverage/mri.2mm/reg.2mm.dat.

My updated command is as followed:
/mri_volcluster *--in* ./sig.${sigFormat} *--thmin* ${thvoxel} 
*--sign* ${sigsignTemp} *--cwpvalthresh 0.05 --minsize* 273 *--fwhm* 6 
*--no-adjust* *--sum* ${nameout}.cluster.summary *--out* 
${nameout}.cluster.nii.gz *--ocn* ${nameout}.ocn.nii.gz *--labelbase* 
$Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_${nameout}/label 
*--reg ${SUBJECTS_DIR}/fsaverage/mri.2mm/reg.2mm.dat* *--mask 
*${SUBJECTS_DIR}/fsaverage/mri.2mm/subcort.mask.mgz/

//
Best,
zhiwei
---
Date: Sat, 25 Nov 2023 14:04:08 -0500
From: "Douglas N. Greve"
Subject: Re: [Freesurfer] No ROI name in summary of MNI305 group
analysis
To:freesurfer@nmr.mgh.harvard.edu
Message-ID:
Content-Type: text/plain; charset="utf-8"

Try adding --reg $SUBJECTS_DIR/fsaverage/mri.2mm/reg.2mm.dat


On 11/23/2023 2:32 AM, wangzhiwei3233 wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Experts,
> I did group-level analysis in MNI305 space.? Then I output the summay 
> via command 'mri_volcluster' as follows:
> /*mri_volcluster --in* ./sig.nii.gz *--thmin* ${thvoxel} *--sign* 
> ${sigsignTemp} *--cwpvalthresh* 0.05 *--minsize* 273 *--fwhm 6* 
> *--no-adjust --sum* ${nameout}.cluster.summary*--out* 
> ${nameout}.cluster.nii.gz *--ocn* ${nameout}.ocn.nii.gz *--labelbase* 
> $Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_${nameout}/label 
> *--mask* 
> /mnt/hgfs/G/work/MetaCog/Human/subjects/fsaverage/mri.2mm/subcort.mask.mgz/

> /
> /
> the output is as follows. there are no ROI names in the table. Is it 
> because I missed the option '--reg' in the command line? Which 
> register file shoul I use if I should add it? I can't find the 
> 'register.dat' file in fsaverage folder.

>
> Very appricated if you can help me.
>
> Best,
> zhiwei

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Re: [Freesurfer] T1 maps longitudinal data

[Douglas N. Greve]

Currently, you'd have to convert them  to  t1-weighted images and then 
run recon-all on that. I think there is software out there to do this if 
you go the t1 maps from an mp2rage scan


On 1/25/2024 11:57 AM, AJ wrote:


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Hi,
I have T1 relaxation maps over 4 time points. In terms of longitudinal 
analysis, could these maps be fed into Freesurfer longitudinal 
pipeline to control for intersubject variability of signal intensity?  
Any other method you would recommend?


Many thanks

AJ

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Re: [Freesurfer] Freesurfer Intensity representation

[Douglas N. Greve]

See this tutorial 
https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0 on 
multimodal integration. Basically, you will need to run mri_vol2vol to 
map your MPF volume to the anatomical/conformed space, then run 
mri_segstats passing it the segmentation you want to use and the 
converted MPF image.


On 1/24/2024 11:04 AM, ERNEST KISSI wrote:


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When MPF images are registered on T1 images, I think the intensity 
represents the MPF values, not the T1 values. This is because the 
registration process only transforms the spatial coordinates of the 
MPF images to match the T1 images, but does not alter the signal 
intensity or contrast of the MPF images. Therefore, the registered MPF 
images still reflect the macromolecular proton fraction of the brain 
tissue, which is independent of the T1 values.


Just wanna confirm. This is from a colleague.

On Wed, Jan 24, 2024 at 6:50 PM ERNEST KISSI 
 wrote:


I want to use the intensity of the macromolecular proton fraction
(MPF). I want to compare the intensity of the MPF of the various
brain regions or structures between two groups. I am not using the
volumes. The MPF was registered  on the T1 so does it mean that
the intensity is from the MPF.

On Wed, Jan 24, 2024 at 6:44 PM ERNEST KISSI
 wrote:

I want to use the intensity of the macromolecular proton
fraction (MPF). I want to compare the intensity of the MPF
between two groups.

On Wed, Jan 24, 2024 at 6:11 PM Fischl, Bruce R.,PHD
 wrote:

It is whatever volume you gave as input to recon-all. If
you tell us which statistics you want to regenerate for
another volume we can tell you know what commands to run.


cheers

Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu
 *On Behalf Of
*ERNEST KISSI
*Sent:* Wednesday, January 24, 2024 9:05 AM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] Freesurfer Intensity representation

*External Email - Use Caution *

Hi,

Please I made an initial enquiry about using freesurfer
for MPF maps. The feedback was that I register the MPF
maps on their corresponding T1 images using multimodal
registration. I used FSL to do the multimodal registration
and then use recon-all in freesurfer.

Now I want to know what the intensity and the volume of
the output in the aseg file represent. Is it the intensity
of the MPF or the TI and MPF?

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Re: [Freesurfer] Recon-all Longitudinal Talairach issue

[Douglas N. Greve]

Can you send the recon-all.log file that contains the error?

On 1/24/2024 4:01 AM, Kapteijns, Kirsten wrote:


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Dear all,

I have run recon-all successfully on multiple subjects on multiple 
timepoints. If I open the mri folder, it shows the correct talairach 
files and no issues arose during processing.


However, when I then run the longitudinal pipeline (first base, which 
also shows correct files) on the subjects (recon-all -long SUBJXXtp1 
SUBJXXbase -all) the talairach shows an failure detection and the 
subsequent file is talairach.invalid.mgz.


The actual segmentation etc. seems fine when inspecting, but when I 
then want to run segmentBS.sh on these processed folders, it gives an 
error.


I have run this a few month back without issue, and had just a few 
subjects left, but now all of them show this same error. Any idea how 
this could be caused?


Kind regards,

Kirsten

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Re: [Freesurfer] Calculation of MRI intensity

[Huang, Yujing]

I think mri_segstats –i option will do that - 
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ERNEST KISSI
Sent: Wednesday, February 7, 2024 8:12 AM
To: Freesurfer support list 
Subject: [Freesurfer] Calculation of MRI intensity


External Email - Use Caution
Hi Freesurfer Team,
Please I want to calculate the mean intensity of a skullstripped MRI image. I 
do not want to use recon-all because I do not want to parcellate or segment it. 
Is there such utility or function in freesurfer?
Thank you.
Sincerely,
Ernest Kissi Kontor.
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Re: [Freesurfer] MRIread and RAS orientation

[Douglas N. Greve]

The vol structure will reflect how the volume is stored on disk. If you 
have two files that have the same structure (ie, order of rows, cols, 
slices) then they will have the same vol in matlab regardless of the 
header orientation.


On 1/23/2024 11:00 AM, Fotiadis, Panagiotis wrote:


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Thank you both! I am asking because I took a nifti file that was in 
RAS orientation (file1), flipped it into LAS (using /fslorient 
-swaporient file2/), and then opened both files in MATLAB with 
MRIread. The resulting .vol matrices for both files were, however, 
identical (i.e., voxel at location  in file1.vol had the exact 
same value as voxel in location  in file2.vol). Would you 
happen to know if the indexing of the vol structure is expected to 
come out the same with MRIread, regardless of the orientation?


Thanks,

Panos

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias 
Gonzalez, Juan E. 

*Date: *Tuesday, January 23, 2024 at 9:14 AM
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] MRIread and RAS orientation

*External Email - Use Caution *

I’m pretty sure that the Matlab code does not reorient.

Cheers,

Eugenio

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 


*Date: *Tuesday, January 23, 2024 at 08:49
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] MRIread and RAS orientation

I’m not sure about the MATLAB codes. When the C codes read in images, 
no automatically transformation is done.


I think you can verify it by checking several [c, r, s] locations of 
both images loaded with MRIread().  I think c and r are reversed in 
MATLAB. And the index starts from 1.


Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Fotiadis, 
Panagiotis

*Sent:* Tuesday, January 23, 2024 1:54 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] MRIread and RAS orientation

*External Email - Use Caution *

Hello,

I have two nifti files that are both in the same MNI space, the former 
of which is saved in LAS orientation while the other in RAS 
orientation (as showcased by the “Orientation” field of mri_info). I 
just wanted to verify: When loading both on MATLAB using MRIread, both 
of their volumes are automatically loaded (or transformed in the case 
of the first file) in the same RAS orientation, right (using the 
vox2ras transformation)?


Thanks in advance!

Best,

Panos

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Re: [Freesurfer] if: Expression Syntax - preproc-sess with -nomc option

[Douglas N. Greve]

Can you run it with -debug as the first option, capture the output, and 
send it to me? It will be a lot of output, so just capture it in a file 
and send the file, eg

preproc-sess -debug -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd 
rest -per-run -sliceorder up -force | tee pps.log



On 1/22/2024 11:20 AM, Stefano Delli Pizzi wrote:
>  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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Re: [Freesurfer] FW: Create a Binarized ROI for Surface

[Douglas N. Greve]

Sorry, I don't understand what you are asking. Can you elaborate?

On 1/19/2024 4:37 PM, Na, Xiaoxu wrote:


External Email - Use Caution

Hi Dr. Doug,

Thanks for your prompt reply!

I’m sorry it was not clear. Basically, I would like to extract the 
cortical volume for each subject using a pre-defined ROI. As I have 
already created the surface ROI, thanks to your answer on the official 
website, I have no further question now on ROI.


This group analysiscan’s further survive the multiple correction using 
the mri_glmfit-sim that you gave me years ago, so there is no file 
like cache.th40.neg.sig.ocn.annot as before.


Instead, I tried to create a ROI and run command line as $mri_segstats 
--seg mask1.sm1.bin.mgh --exlude 0 --i 
groupAnalysis/lh.volume.g2v2.10.mgh --avgwf lh.volume.mask1.dat, where 
mask1.sm1.bin.mgh is the ROI and groupAnalysis/lh.volume.g2v2.10.mgh 
is the mris_proc processed file from a group of subjects. It did 
extract something, 1 number for each subject, but I believe there is a 
ratio or scalar between the actual volume of that vertex and those 
show in lh.volume.g2v2.10.mgh. Is there anywhere I can figure out 
where this ratio/scalar is? Thank you so much!


Regards,

Xiaoxu

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* Friday, January 19, 2024 3:16 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] FW: Create a Binarized ROI for Surface

On 1/19/2024 3: 45 PM, Na, Xiaoxu wrote: External Email - Use Caution 
Dear Freesurfer Expert, While the sphere can only be drawn using that 
Dr. Doug suggested, the sphere option would mess up. Do you need help 
with this? If so, can you give


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On 1/19/2024 3:45 PM, Na, Xiaoxu wrote:

*External Email - Use Caution *

Dear Freesurfer Expert,

While the sphere can only be drawn using that Dr. Doug  suggested,
the sphere option would mess up.

Do you need help with this? If so, can you give more info?

I have a further question as using this ROI to extract surface
information from ?h.area and ?h.volume. I’m using the command line
as below:

$mri_segstats --seg mask1.sm1.bin.mgh --exlude 0 --i
groupAnalysis/lh.volume.g2v2.10.mgh --sumwf lh.volume.mask1.dat

However, due to the calculation of surface and volume, we need
another input of sum file (ASCII file), how can I do that before I
can run the above?

Sorry, I don't know what you mean

Another simple question is, what is lh.volume.mgh in the group
analysis folder processed by mris_proc? Is that a simple merge of
all subjects lh.volume file? Why the number is between 0-10, is
there any way I can put ?h.volume or ?h.area back to gain each
subject’s real volume or area value on that surface vertex? Thank
you so much!

This is a vertex-wise measure of volume of the cortex at that point. 
Eg, a given vertex has an area defined by the mean area of the 
triangles that abut it. When this  is multiplied by the thickness, you 
get a volume measure (we actually compute it differently using a 
truncated pyramid, but that's the basic idea). You can use this in a 
VBM-like analysis.


Regards,

Xiaoxu

*From:* Na, Xiaoxu
*Sent:* Wednesday, December 13, 2023 4:25 PM
*To:* Freesurfer support list 

*Subject:* Create a Binarized ROI for Surface

Dear Freesurfer Expert,

We would like to extract mean Cth values for each subject within a
own-creaded ROI (surface defined), using freeview (for instance).
Is it possible to create a ROI (i.e. spherical surface)
surrounding a particular vertex of an sig.mgh file? (and then
extract its mean Cth values for each subject)?

I think this is not a new question, and it was posted somehow on
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers

Re: [Freesurfer] make_average_subject command error

[Huang, Yujing]

If you run recon-all, ?h.pial will appear as symbolic links to ?h.pial.T1.  
Here is the list of symbolic links you should find in your subject/surf 
directory:

rh.pial -> rh.pial.T1
lh.pial -> lh.pial.T1
rh.fsaverage.sphere.reg -> rh.sphere.reg
lh.fsaverage.sphere.reg -> lh.sphere.reg
rh.white.K -> rh.white.preaparc.K
rh.white.H -> rh.white.preaparc.H
lh.white.K -> lh.white.preaparc.K
lh.white.H -> lh.white.preaparc.H

I'm wondering why the symbolic links are not created.

To create the symbolic links,
1. cd to subject/surf directory
2. run ln command to create each link, for example, 'ln -s lh.pial.T1 lh.pial'

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Asuka Toyofuku
Sent: Wednesday, February 7, 2024 5:13 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] make_average_subject command error


External Email - Use Caution

Dear Freesurfer experts,



We're trying to make an average subject for group analysis using Freesurfer 
7.1, but the make_average_subject command exits with errors after calling 
make_average_surf:


MakeAverageSurf(): 129 lh pial sphere.reg talairach.xfm 1 1


It appears to be trying to find the lh.pial surface for the first participant, 
but this file is named "lh.pial.T1". (In FS 5.3 and 6.0, this file was labelled 
"lh.pial", but with FS7.1, it seems to be named lh.pial.T1).


Does anyone have a suggestion for how to fix this problem? (We want to avoid 
changing all the file names to "lh.pial" from "il.pial.T1")
Should we call make_average_subject again with -no-surf-to-surf ?

Best regards,
Asuka
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[Freesurfer] Calculation of MRI intensity

[ERNEST KISSI]

External Email - Use Caution

Hi Freesurfer Team,

Please I want to calculate the mean intensity of a skullstripped MRI image.
I do not want to use recon-all because I do not want to parcellate or
segment it. Is there such utility or function in freesurfer?

Thank you.

Sincerely,
Ernest Kissi Kontor.
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freesurfer recon-all qcache partial failure

[Asuka Toyofuku]

External Email - Use Caution

Dear Yujing,

Thank you for your kind help (and sorry for my late reply).
It worked with the added flag; - measures thickness.
I appreciate your advice on adding directives at the end of the recon-all 
command.

Best,
Asuka

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: 16 January 2024 13:41
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure


The command should look like this ‘recon-all -s subjid -qcache -all -i 
input-file’





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Asuka Toyofuku
Sent: Monday, January 15, 2024 9:45 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure



External Email - Use Caution

Dear Yujing,



Thank you very much for your kind help.



So, you're saying I need more directive other than -qcashe?

My command was;

for d in Te* te* EPK* epk*

do recon-all -s $d -qcache

done



Do you think I should add another directive, such as -all or -autorecon-all?

So, the command line looks like this?

recon-all -s -subjid -qcashe - autorecon-all



I ran recon-all -qcashe not on the fsaverage folder, but in the SUBJECT_DIR.

In the previous post, I attached the wrong recon-all log (which was from 
fsaverage>scripts folder), but now I'm attaching the recon-all log file from a 
random subject folder.

Could you please look and check this recon-all as well?

Many thanks!



Best,

Asuka





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: 12 January 2024 14:24
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure



Your recon-all command doesn’t have the directive to tell it what to run. You 
also need to specify input files for your initial run.  See this wiki page for 
detail MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1WHtKoBRWRweL9tOk04WS_fJMQNq-6FmCk7jSMyjZxjX34yU-Dlr5b4MzSwJL0G4PCxBUEWet96Y3jjqc8Eg-MkfKhwWflyMuhk9fmnVywIMKVjjl3LCipveJDkFaKnkM_qJ3ZE4TUygho39aVC6uloeAdYv3L3E1RgcAfLZ66tZhKh6x41SPMkse4TUZNWr7qUY6z5ebLWoZYv8vnwoKlxK40EFn409Puic2n3fgLNZZOvEb99nWSNV3_rFb3lo7l29NkdLmDJzD7xafSmiEzetkbSw7Db1ENHv8B_2bVA5S5Zt2oBdDE8fBRfMMl4gs/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all



The recon-all.log attached contains runs between 2009 and 2010 on subject 
‘fsaverage’.



‘fsaverage’ is an average subject comes with Freesurfer distribution in 
$FREESURFER_HOME/subjects/. fsaverage is a template brain based on a 
combination of 40 MRI scans of real brains. It can be used as a common space 
for group comparison. You don’t want to run recon-all on it.



Your SUBJECTS_DIR should not set to your Freesurfer download/install directory. 
Set it to some other directory where you have the write permission.



You should see ‘fsaverage’ as a symbolic link in your SUBJECTS_DIR.



Best,



Yujing







From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Asuka Toyofuku
Sent: Friday, January 12, 2024 4:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer recon-all qcache partial failure



External Email - Use Caution

Dear Freesurfer researchers,



I have an issue with recon-all-qcashe results. (please find the recon-all.log 
attached.)

The command created fsaverage mgh files (e.g., lh.thickness.fsaverage.mgh), but 
it did not create fsaverage files with different smoothing levels (e.g.,  
lh.thickness.fwhm10.fsaverage.mgh, lh.thickness.fwhm15.fsaverage.mgh, 
lh.thickness.fwhm20.fsaverage.mgh...etc) in the individual subject "surf" 
folder.



I used the command below:

for d in Te* te* EPK* epk*

do recon-all -s $d -qcache

done



(Subjects names start from either Te, te, EPK or epk)

For several subjects with failed recon-all commands, I re-ran the command 
individually:

 recon-all -s subjectname -qcashe



(output from the terminal window)

It could also be that recon-all was running at one point but died in an 
unexpected way.

If it is the case that there is a process running, you can kill it and start 
over or ju

Re: [Freesurfer] Command terminated by signal 11 when execute mris_place_surface

[Yp Ben]

External Email - Use Caution

Hello freesurfer experts ,
I change the command and reduce the threads from 200 to 50 , seems ok now ,
I use the cluster to run the jobs and submit jobs to cluster, I found there
have several jobs assigned to the same node , do this be ok to run
different subjects in one node with the same time ? Thanks.

Yp Ben  于2024年2月6日周二 13:39写道：

> Hello FreeSurfer Developers,
>
> I'm want to run HCP T1W data of recon-all , but it always failed on step
> " WhitePreAparc lh", below is my run information:
> OS: Ubuntu 22.04.2 LTS
> MEM: 32G
> CPU: 16
>
> Freesurfer Version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
>
> Command:
> export SUBJECTS_DIR=$(pwd)
> nohup recon-all -s $1 -i $(ls *${1}*) -all -qcache -3T -parallel -openmp
> 16 -threads 200 > nohup_${1}.log 2> nohup_${1}.log &
>
> Error messages as below:
> mris_autodet_gwstats done
> @#@FSTIME  2024:02:06:05:28:14 mris_autodet_gwstats N 8 e 5.75 S 1.02 U
> 8.70 P 169% M 277604 F 3 R 131626 W 0 c 403 w 6466 I 0 O 8 L 1.96 14.01
> 13.54
> @#@FSLOADPOST 2024:02:06:05:28:20 mris_autodet_gwstats N 8 1.96 13.81 13.47
> #
> #@# WhitePreAparc lh 2024年 02月 06日 星期二 05:28:20 CST
> cd /home/tben/ds000102/HCA6139970_V1_MR/mri
> mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz
> --threads 200 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o
> ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
> 7.4.1
> 7.4.1
>
> cd /home/tben/ds000102/HCA6139970_V1_MR/mri
> setenv SUBJECTS_DIR /home/tben/ds000102
> mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz
> --threads 200 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o
> ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
>
> Command terminated by signal 11
> @#@FSTIME  2024:02:06:05:28:20 mris_place_surface N 18 e 24.22 S 4.47 U
> 1.71 P 25% M 185596 F 9 R 46047 W 0 c 184 w 12734 I 1296 O 0 L 1.96 13.81
> 13.47
> @#@FSLOADPOST 2024:02:06:05:28:44 mris_place_surface N 18 69.96 28.86 18.46
> Linux tben-dev-server 6.5.0-15-generic #15~22.04.1-Ubuntu SMP
> PREEMPT_DYNAMIC Fri Jan 12 18:54:30 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s HCA6139970_V1_MR exited with ERRORS at 2024年 02月 06日 星期二
> 05:28:45 CST
>
> For more details, see the log file
> /home/tben/ds000102/HCA6139970_V1_MR/scripts/recon-all.log
> To report a problem, see
> http://secure-web.cisco.com/1soATQZ1AnuA1BePnpvsKZY6noRO1D_NKP3ktYxdGpbc46jBBfb66Kk98nQEd7cToAZ6xkufBDAKaKj5XLVlmrIynx34OuetEvx16iA_ThaYlazxCjgmHQSI1HNVHJYpFCVCyIXo09mcghcvrig74kIa8IJ_ZOswsGw26wXfp-uVF8_uqzISA12elH7ySeiKMSeUzlFkwRbB914-sYkfzS-GCYEsFOJ9edd9ADaXEd5h4fF19wOVzezr1402ZtXv9QRui034tHyTU45jCYH_FARrGm-k6T4P-MTamv9JkFWxBr2mv54wRbVir8NRVFEFD/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
>
>
> Check the core dump file under /var/crash
> vim _opt_freesurfer_bin_mris_place_surface.1000.crash
> ProcStatus:
>  Name:  mris_place_surf
>  Umask: 0002
>  State: S (sleeping)
>  Tgid:  23410
>  Ngid:  0
>  Pid:   23410
>  PPid:  22657
>  TracerPid: 0
>  Uid:   1000100010001000
>  Gid:   1000100010001000
>  FDSize:64
>  Groups:4 24 27 30 46 122 134 135 1000
>  NStgid:23410
>  NSpid: 23410
>  NSpgid:23410
>  NSsid: 22657
>  Kthread:   0
>  VmPeak:10878292 kB
>  VmSize:10394436 kB
>  VmLck:0 kB
>  VmPin:0 kB
>  VmHWM:   185500 kB
>  VmRSS:   185500 kB
>  RssAnon: 179356 kB
>  RssFile:   6144 kB
>  RssShmem: 0 kB
>  VmData: 2068316 kB
>  VmStk:  132 kB
>  VmExe: 3084 kB
>  VmLib: 3820 kB
>  VmPTE: 1772 kB
>  VmSwap:   0 kB
>  HugetlbPages: 0 kB
>  CoreDumping:   1
>  THP_enabled:   1
>  untag_mask:0x
>  Threads:   200 SigQ:  0/128234
>  SigPnd:
>  ShdPnd:
>  SigBlk:
>  SigIgn:
>  SigCgt:0001
>  CapInh:
>  CapPrm:
>  CapEff:
>  CapBnd:01ff
>  CapAmb:
>  NoNewPrivs:0
>  Seccomp:   0
>  Seccomp_filters:   0
>  Speculation_Store_Bypass:  thread vulnerable
>  SpeculationIndirectBranch: conditional enabled
>  Cpus_allowed:  
>  Cpus_allowed_list: 0-15
>  Mems_allowed:
>  
> ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0003
>  Mems_allowed_list: 0-1
>  voluntary_ctxt_switches:   21
>  nonvoluntary_ctxt_switches:17
> Signal: 11
> Uname: Linux 6.5.0-15-generic x86_64
> UserGroups: adm cdrom dip lpadmin lxd p

[Freesurfer] make_average_subject command error

[Asuka Toyofuku]

External Email - Use Caution

Dear Freesurfer experts,


We're trying to make an average subject for group analysis using Freesurfer 
7.1, but the make_average_subject command exits with errors after calling 
make_average_surf:


MakeAverageSurf(): 129 lh pial sphere.reg talairach.xfm 1 1


It appears to be trying to find the lh.pial surface for the first participant, 
but this file is named "lh.pial.T1". (In FS 5.3 and 6.0, this file was labelled 
"lh.pial", but with FS7.1, it seems to be named lh.pial.T1).


Does anyone have a suggestion for how to fix this problem? (We want to avoid 
changing all the file names to "lh.pial" from "il.pial.T1")
Should we call make_average_subject again with -no-surf-to-surf ?

Best regards,
Asuka
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
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