[Freesurfer] Issue with cortical data extraction for mkanalysis-sess

[O'Dor, Sarah]

We are trying to run resting state connectivity analyses using amygdala ROI. 
The left hemisphere ran fine, but for the right hemisphere, something is 
clearly off. When we export the results into a table, the unknown column, which 
should be zero, has values, and one of the regions instead has zeroes. It’s as 
if something is shifted, but we’ve checking the coding. Briefly, the commands 
we used were mri_vol2vol, fcseed-config, fcseed-sess, mkanalysis-sess, 
selxavg3-sess, mri_glmfit, mri_segstats. Any ideas on where/which commend we 
should be troubleshooting? We’ve run it twice and gotten the same results.

Thanks,
Sarah
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Re: [Freesurfer] Bug in mri_convert reslice-like with 4D images

[fsbuild]

External Email - Use Caution

It could help to see the core dump file. If you are on a Mac it 
will probably display it. If you are on Linux and you have core dumps 
enabled on the system, then you have to look in the logs.
- R.

On Jun 6, 2024, at 15:56, Iglesias Gonzalez, Juan E. 
jiglesiasgonza...@mgh..harvard.edu wrote:Dear FS experts,We get a 
segfault when I try to resample images with the command:mri_convert input.mgz 
output.mgz -rl reference..mgzwhen reference.mgz has multiple frames 
(e.g., a RGB volume). Any idea of why this is happening?Cheers,/Eugenio 
(Stefano  
Pranav)___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] negative values converting mgz files to nifty

[Nina Rouhani]

External Email - Use Caution

hello!

after freesurfer segmentation (through fmriprep v23), i converted the
aparc+aseg.mgz file into a nifty file using the below code (freesurfer
v7.4.1):
-rl $fs_dir/mri/rawavg.mgz
-rt nearest $fs_dir/mri/aparc+aseg.mgz
$sub_dir/rois/anatomical/aparc_aseg2mprage.nii.gz

however, the voxel values of the aparc_aseg2mprage.nii.gz range between
31000-32000 and -31000- -32000. consequently, the label values for
particular regions no longer correspond to what’s in the freesurfer manuals
(like those listed here: FsTutorial/AnatomicalROI/FreeSurferColorLUT - Free
Surfer Wiki

).

would be incredibly grateful if i could be pointed to what i’m missing or
what could be going wrong! thank you!
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[Freesurfer] Bug in mri_convert reslice-like with 4D images

[Iglesias Gonzalez, Juan E.]

Dear FS experts,
We get a segfault when I try to resample images with the command:
mri_convert input.mgz output.mgz -rl reference.mgz
when reference.mgz has multiple frames (e.g., a RGB volume). Any idea of why 
this is happening?
Cheers,
/Eugenio ( & Pranav)
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[Freesurfer] Incoporating synthstrip and synthseg into recon-all

[Dan Levitas]

External Email - Use Caution

Hello,

I am using freesurfer version 7.4.1, and would like to incorporate the
recently introduced synthstrip and synthseg functions into my recon-all
command, if that's possible. From this archive message (
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg75148.html)
it seems that adding the -synthstrip option enables synthstrip; however, I
don't see this as an option in the recon-all documentation (
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all) nor as a command line
option for recon-all.

Assuming that both synthstrip and synthseg can be used in recon-all, would
the command need to look something like this:
*recon-all -subjid sub-${sub}_ses-${ses} -i $anat_file -3T -synthstrip
--no-csf -synthseg -qcache -all*

I'm adding the *--no-csf* synthstrip option based on this comment (
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg75172.html).

I should also note that I'm performing a longitudinal analysis, so this
specific recon-all pertains to the cross-sectional portion of the workflow.

Thanks,

Dan
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Re: [Freesurfer] fs_temp_file: Command not found

[Huang, Yujing]

'fs_temp_file' should be in the same directory as recon-all.  Can you check if 
it exists -  'ls -l $FREESURFER_HOME/bin/fs_temp_file'?

Also,  '/Applications/freesurfer/7.4.1/subjects' is part of Freesurfer 
distribution. You should change SUBJECTS_DIR to point to some other directory 
you have write permission.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Cameron, Jack
Sent: Thursday, June 6, 2024 9:36 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] fs_temp_file: Command not found


External Email - Use Caution
Hello FreeSurfer developers,

I am in the process of learning how to use FreeSurfer and attempting to run the 
recon-all on FreeSurfer 7.4.1 on a 2019 MacBook Pro (Sonoma 14.5).

The response is attached as a pdf, but I have also copied and pasted the 
environment and commands below.


Last login: Thu Jun  6 14:07:57 on ttys000
jack@Jack-MacBook-Pro ~ % export FREESURFER_HOME=/Applications/freesurfer/7.4.1
jack@Jack-MacBook-Pro ~ % export SUBJECTS_DIR=$FREESURFER_HOME/subjects
jack@Jack-MacBook-Pro ~ % echo $FREESURFER_HOME
/Applications/freesurfer/7.4.1
jack@Jack-MacBook-Pro ~ % echo $SUBJECTS_DIR
/Applications/freesurfer/7.4.1/subjects
jack@Jack-MacBook-Pro ~ % source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.4.1
FSFAST_HOME   /Applications/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.4.1/subjects
MNI_DIR   /Applications/freesurfer/7.4.1/mni
jack@Jack-MacBook-Pro ~ % which freeview
/Applications/freesurfer/7.4.1/bin/freeview
jack@Jack-MacBook-Pro ~ % which recon-all
/Applications/freesurfer/7.4.1/bin/recon-all
jack@Jack-MacBook-Pro ~ % cd SUBJECTS_DIR
cd: no such file or directory: SUBJECTS_DIR
jack@Jack-MacBook-Pro ~ % cd $SUBJECTS_DIR
jack@Jack-MacBook-Pro subjects % ls
HYPE_shared cvs_avg35_inMNI152 fsaverage_sym
README fsaverage lh.EC_average
Test.nii fsaverage3 rh.EC_average
V1_average fsaverage4 sample-001.mgz
bert fsaverage5 sample-002.mgz
cvs_avg35 fsaverage6 tutorial_data_20190918_1558
jack@Jack-MacBook-Pro subjects % recon-all -all -i sample-001.mgz -s SAMPLE001J6
fs_temp_file: Command not found.
fs-check-version --s SAMPLE001J6 --o
ERROR: flag --o requires one argument
I see that there is not an EXIT as is typical with FreeSurfer hard failures... 
Do you have any advice on where I might have gone wrong? I could not find any 
information posted/previous issues with this command online.

I appreciate any help you can provide.



Jack
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[Freesurfer] fs_temp_file: Command not found

[Cameron, Jack]

External Email - Use Caution

Hello FreeSurfer developers,

I am in the process of learning how to use FreeSurfer and attempting to run the 
recon-all on FreeSurfer 7.4.1 on a 2019 MacBook Pro (Sonoma 14.5).

The response is attached as a pdf, but I have also copied and pasted the 
environment and commands below.


Last login: Thu Jun  6 14:07:57 on ttys000
jack@Jack-MacBook-Pro ~ % export FREESURFER_HOME=/Applications/freesurfer/7.4.1
jack@Jack-MacBook-Pro ~ % export SUBJECTS_DIR=$FREESURFER_HOME/subjects
jack@Jack-MacBook-Pro ~ % echo $FREESURFER_HOME
/Applications/freesurfer/7.4.1
jack@Jack-MacBook-Pro ~ % echo $SUBJECTS_DIR
/Applications/freesurfer/7.4.1/subjects
jack@Jack-MacBook-Pro ~ % source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.4.1
FSFAST_HOME   /Applications/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.4.1/subjects
MNI_DIR   /Applications/freesurfer/7.4.1/mni
jack@Jack-MacBook-Pro ~ % which freeview
/Applications/freesurfer/7.4.1/bin/freeview
jack@Jack-MacBook-Pro ~ % which recon-all
/Applications/freesurfer/7.4.1/bin/recon-all
jack@Jack-MacBook-Pro ~ % cd SUBJECTS_DIR
cd: no such file or directory: SUBJECTS_DIR
jack@Jack-MacBook-Pro ~ % cd $SUBJECTS_DIR
jack@Jack-MacBook-Pro subjects % ls
HYPE_shared cvs_avg35_inMNI152 fsaverage_sym
README fsaverage lh.EC_average
Test.nii fsaverage3 rh.EC_average
V1_average fsaverage4 sample-001.mgz
bert fsaverage5 sample-002.mgz
cvs_avg35 fsaverage6 tutorial_data_20190918_1558
jack@Jack-MacBook-Pro subjects % recon-all -all -i sample-001.mgz -s SAMPLE001J6
fs_temp_file: Command not found.
fs-check-version --s SAMPLE001J6 --o
ERROR: flag --o requires one argument

I see that there is not an EXIT as is typical with FreeSurfer hard failures... 
Do you have any advice on where I might have gone wrong? I could not find any 
information posted/previous issues with this command online.

I appreciate any help you can provide.



Jack


fs_temp_file-Command not found.pdf
Description: fs_temp_file-Command not found.pdf
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Re: [Freesurfer] Freesurfer license

[Wighton, Paul]

Hi Liz,

Can you try adding a `-B ` to the `singularity 
run` command?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ayoub, Lizbeth 

Sent: Monday, June 3, 2024 2:53 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer license

Thank you Paul, I am using fmriprep-32.1.4.simg, and built it using this 
command:

singularity build ./fmriprep-23.1.4.simg docker://nipreps/fmriprep:23.1.4

I use this command to run fMRIprep:

singularity run --nv --cleanenv -B  -B   -B  -B   -w  --output-spaces 
{MNI152NLin2009cAsym:res-1,T1w:res-1} --ignore slicetiming --fs-license-file 
   
participant --participant_label  --skip-bids-validation

The only error I am getting is for the freesurfer license file location: 
--fs-license-file 

ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked 
for an existing license file at several paths, in this order: 1) command line 
argument ``--fs-license-file``; 2) ``$FS_LICENSE`` environment variable; and 3) 
the ``$FREESURFER_HOME/license.txt`` path. Get it (for free) by registering at 
https://surfer.nmr.mgh.harvard.edu/registration.html


thank you!!

L

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wighton, Paul 

Sent: Monday, June 3, 2024 12:33 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer license

Hi Liz,

What fmriprep container are you using and what are the full commands that are 
not working?

Are you bind-mounting the freesurfer license file into the container via 
`singularity exec --bind`?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ayoub, Lizbeth 

Sent: Monday, June 3, 2024 11:48 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer license

Hi,

I am using singularity to run fmriprep, and it seems that it is not recognizing 
the location of my freesurfer license ( it is a new license). I have tried all 
three options for location, and none work:

ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked 
for an existing license file at several paths, in this order: 1) command line 
argument ``--fs-license-file``; 2) ``$FS_LICENSE`` environment variable; and 3) 
the ``$FREESURFER_HOME/license.txt`` path. Get it (for free) by registering at 
https://surfer.nmr.mgh.harvard.edu/registration.html

I appreciate any insights on how to fix this error :)

Thank you so much,

Liz











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Re: [Freesurfer] mri_fuse_segmentation error: could not open file

[Tommaso Cusolito S319624]

External Email - Use Caution

Hello FreeSurfer Developers,

I have explored a possible solution to my problem which would include 
coregistering my fifth scan to the template extracted from the first 
four scans through the function mri_coreg (described at: 
https://freesurfer.net/fswiki/mri_coreg). Although the function is 
listed on the website, it comes up as non existent when called.

Is it deprecated? Is there a viable alternative which someone has 
explored?



Il 2024-05-24 12:51 Tommaso Cusolito S319624 ha scritto:
> External Email - Use Caution
> 
> Hello FreeSurfer Developers,
> 
> I'm attempting to extract cortical thickness from a fifth scan using a
> template based on only the first four scans (obtained by following the
> longitudinal pipeline available at
> https://secure-web.cisco.com/1S7BQNmF9HghVT1XkcD-pYvMmoQDm0WTjg3-N1bP-4anPWQecP6BcEe1Czg5O1f2CwxkS5g6wvBC5ciP3B6fZBjHEArdfmqkQIDI1Gm7n0lLp1tjx4D4zvFYVzpSisw5KdAUrOc5MOZaTWLk0Hb2-gonhx3sqwRsmkWBznF1VYEORhfrW8ssC8QJg1j-KOTVg7occo24GF3AoarScmNgUSRTCutAjK6UGSDw2qbjT0jnd9Tmvg2TkPeAJETtQcmz2aYGEd5Pj7fs45UUqJB22CSonXUlpevMHJJfWtDO2FfuZm8dH-TQjj4u9kz8qeovL/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing).
> Unfortunately, I don't have the option to run the longitudinal
> processing from scratch including the fifth scan as I no longer have
> access to the cross-sectionally processed single scan data (in format
> patient_scan#) for scans 1 through 4 but only to the folders generated
> by the recon-all function (in format
> patient_scan#.long.patient_template).
> I've made sure to generate .lta files (through mri_robust_register)
> for forwards and backwards transformations from s5 to template and to
> add the scan 5 to the "base-tps" file, but recon-all reports a later
> error when using the function mri_fuse_segmentations as I no longer
> have access to files for single scans (norm.mgz,
> aseg.mgz,aseg.auto_noCCseg.mgz).
> I acknowledge that the template data will be biased towards the first
> four scans but I was looking for a way to use the function on only
> data belonging to the "patient_scan#.long.patient_template" folders
> together with the fifth scan data "patient_s5".
> 
> Has anyone tried using this course of action and found a viable 
> solution?
> 
> I've attached the recon-all.log in case it's of any use.
> 
> 1) FreeSurfer version: 
> freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> 
> 2) Platform: 3.10.0-1160.92.1.el7.x86_64
> 
> 3) uname -a: Linux krusty 3.10.0-1160.92.1.el7.x86_64 #1 SMP Tue Jun
> 20 11:48:01 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
> 
> 4) recon-all.log: see attached
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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.

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Re: [Freesurfer] Freesurfer license

[Ayoub, Lizbeth]

Thank you Paul, I am using fmriprep-32.1.4.simg, and built it using this 
command:

singularity build ./fmriprep-23.1.4.simg docker://nipreps/fmriprep:23.1.4

I use this command to run fMRIprep:

singularity run --nv --cleanenv -B  -B   -B  -B   -w  --output-spaces 
{MNI152NLin2009cAsym:res-1,T1w:res-1} --ignore slicetiming --fs-license-file 
   
participant --participant_label  --skip-bids-validation

The only error I am getting is for the freesurfer license file location: 
--fs-license-file 

ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked 
for an existing license file at several paths, in this order: 1) command line 
argument ``--fs-license-file``; 2) ``$FS_LICENSE`` environment variable; and 3) 
the ``$FREESURFER_HOME/license.txt`` path. Get it (for free) by registering at 
https://surfer.nmr.mgh.harvard.edu/registration.html


thank you!!

L

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wighton, Paul 

Sent: Monday, June 3, 2024 12:33 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer license

Hi Liz,

What fmriprep container are you using and what are the full commands that are 
not working?

Are you bind-mounting the freesurfer license file into the container via 
`singularity exec --bind`?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ayoub, Lizbeth 

Sent: Monday, June 3, 2024 11:48 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer license

Hi,

I am using singularity to run fmriprep, and it seems that it is not recognizing 
the location of my freesurfer license ( it is a new license). I have tried all 
three options for location, and none work:

ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked 
for an existing license file at several paths, in this order: 1) command line 
argument ``--fs-license-file``; 2) ``$FS_LICENSE`` environment variable; and 3) 
the ``$FREESURFER_HOME/license.txt`` path. Get it (for free) by registering at 
https://surfer.nmr.mgh.harvard.edu/registration.html

I appreciate any insights on how to fix this error :)

Thank you so much,

Liz











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[Freesurfer] fmriprep and freesurfer license

[Patterson, Dianne K - (dkp)]

External Email - Use Caution

I use this on our HPC:

apptainer run --cleanenv --bind ${MRIS}/data:/data:ro  --bind 
${MRIS}/derivatives/fmriprep:/outputs --bind ${MRIS}/fmriprep_work:/work ${APP} 
/data /outputs participant --participant_label ${Subject} --fs-license-file 
${HOME}/license.txt -w /work  --stop-on-first-crash --ignore slicetiming 
--cifti-output --output-spaces fsnative fsaverage MNI152NLin6Asym:res-2

This assumes license.txt is in my home directory.

-Dianne

Dianne Patterson, Ph.D
d...@arizona.edu
Office: BSRL, Room 235
RII Neuroimaging Staff Scientist
Program Coordinator Neuroimaging Methods 
Certificate
Cognitive Science GIDP affiliate member
Faculty Lead OpenClass.ai
Mastodon: @d...@scicomm.xyz
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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

[Douglas N. Greve]

If it is only one subject and you have no continuous variables, you can 
do it that way. If you have continuous variables, you will need to use 
DOSS (different-offset same slope) to force the slopes to be the same 
across classes (because you can't compute a slope from a single data point)


On 5/10/2024 12:46 PM, Liliana Wu wrote:


External Email - Use Caution

Thank you Douglas. That’s much clearer. I do however,  have a subject 
without a gender disclosure. Would I set up my class and contrasts as:


5 classes: PatentientsMale, PatientsFemale, HCMale, HCFemale, HCNa

then use contrast [0.5 0.5 -0.33 -0.33 -0.33 0 0 0 0 0 ...]?

Best,

Liliana


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Re: [Freesurfer] Recon-all for a common template

[Douglas N. Greve]

Why did you do an lr reversal if it looked good? And when you say it 
looks good, what do you mean. One thing to double check is that the 
orientation looks ok. Load it in freeview. Up at the top you will see 
little brain images in coronal, sagital, and axial. When you click on 
one of those, the brain in the main image should become coronal, sag, or 
axial. If this does not happen, then something is wrong.

On 5/29/2024 10:47 AM, Chen Yang wrote:
>  External Email - Use Caution
>
> Hi Douglas,
>
> thanks so much for you reply. Yes, I checked the template and it looks good. 
> The orientation was in LAS originally then I did the Left-Right Reversal by 
> using the command "mri_convert --in_orientation RIA". Before or after the 
> reversal, I got the same error message. Here I attached the template, could 
> you please have a look in case of any clue? Thank you so much!
>
> Best,
> Chen
>
>   
>
> - Original Message -
>> From: "Douglas N. Greve" 
>> To: "freesurfer" 
>> Sent: Wednesday, 29 May, 2024 15:26:25
>> Subject: Re: [Freesurfer] Recon-all for a common template
>> sounds like something is wrong with the image. Did you look at
>> ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a
>> head?
>>
>> On 5/28/2024 6:07 AM, Chen Yang wrote:
>>>   External Email - Use Caution
>>>
>>> Hi everyone,
>>>
>>> I tried to run the reconstruction with the command line:  recon-all -i
>>> ANTS_QS_template_MNI.nii.gz -subject CGBT -all
>>>
>>> then I got the error message:
>>> talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
>>> talairach_avi log file is transforms/talairach_avi.log...
>>> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
>>> Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64
>>> GNU/Linux
>>>
>>> And this is the error message in the talairach_avi.log:
>>> imgrege: no voxels in register
>>> ERROR: 'imgreg_4dfp
>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305
>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask
>>> talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed!
>>> status=254
>>> ERROR: mpr2mni305 execution aborted
>>>
>>> Does anyone know how to solve this problem? Thanks so much!
>>>
>>> Best,
>>> Chen
>>> - Original Message -
 From: "Chen Yang" 
 To: "freesurfer" 
 Sent: Monday, 20 May, 2024 13:59:13
 Subject: [Freesurfer] Recon-all for a common template
 External Email - Use Caution

 Dear Freesurfer Developers,

 my data is from 50 preschoolers and I created my own group template from 
 these
 kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti 
 file
 (see attached). Then we'd like to process this group template in 
 Freesurfer to
 reconstruct the cortical surfaces as the individual brain images. My 
 question
 is, how can i do the recon-all with the template? Because I only have this
 template file I feel I don't have enough input files(?).

 Thanks in advance!

 Best regards,
 Chen

 --
 Chen Yang

 PhD Student
 Independent Research Group 'Milestones of Early Childhood Development'
 Max Planck Institute for Human Cognitive and Brain Sciences

 Email:ya...@cbs.mpg.de

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Re: [Freesurfer] How to get the parcellations to the initial space as before running recon all

[Douglas N. Greve]

Does this web site 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat cover 
what you need to do?


On 6/3/2024 10:58 AM, Reji, A. (Amal, Student M-EE) wrote:


External Email - Use Caution

Hi,
    I was trying to get the mesh files for cortical parcellations 
after running recon all. I used the Ernie data set which is the 
example dataset given by SimNIBS. 
 I did 
recon all to the Ernie dataset and I got the parcellations. Now I want 
to get these parcellations to the same space as the space of Ernie. 
How can I convert the parcellations in the initial space?

Looing forward to hearing from you
Regards
Amal Reji

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Re: [Freesurfer] Freesurfer license

[Wighton, Paul]

Hi Liz,

What fmriprep container are you using and what are the full commands that are 
not working?

Are you bind-mounting the freesurfer license file into the container via 
`singularity exec --bind`?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ayoub, Lizbeth 

Sent: Monday, June 3, 2024 11:48 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer license

Hi,

I am using singularity to run fmriprep, and it seems that it is not recognizing 
the location of my freesurfer license ( it is a new license). I have tried all 
three options for location, and none work:

ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked 
for an existing license file at several paths, in this order: 1) command line 
argument ``--fs-license-file``; 2) ``$FS_LICENSE`` environment variable; and 3) 
the ``$FREESURFER_HOME/license.txt`` path. Get it (for free) by registering at 
https://surfer.nmr.mgh.harvard.edu/registration.html

I appreciate any insights on how to fix this error :)

Thank you so much,

Liz











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[Freesurfer] Freesurfer license

[Ayoub, Lizbeth]

Hi,

I am using singularity to run fmriprep, and it seems that it is not recognizing 
the location of my freesurfer license ( it is a new license). I have tried all 
three options for location, and none work:

ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked 
for an existing license file at several paths, in this order: 1) command line 
argument ``--fs-license-file``; 2) ``$FS_LICENSE`` environment variable; and 3) 
the ``$FREESURFER_HOME/license.txt`` path. Get it (for free) by registering at 
https://surfer.nmr.mgh.harvard.edu/registration.html

I appreciate any insights on how to fix this error :)

Thank you so much,

Liz










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[Freesurfer] How to get the parcellations to the initial space as before running recon all

[Reji, A. (Amal, Student M-EE)]

External Email - Use Caution

Hi,
I was trying to get the mesh files for cortical parcellations after running 
recon all. I used the Ernie data set which is the example dataset given by 
SimNIBS. I did recon 
all to the Ernie dataset and I got the parcellations. Now I want to get these 
parcellations to the same space as the space of Ernie. How can I convert the 
parcellations in the initial space?
Looing forward to hearing from you
Regards
Amal Reji
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[Freesurfer] Call for applications: LINC fellows program 2024-25

[Yendiki, Anastasia]

Dear FreeSurfers - Our BRAIN Initiative funded center for Large-scale Imaging 
of Neural Circuits (LINC) is seeking to name 
2 undergrads and 2 postdocs from diverse backgrounds and/or under-resourced 
institutions “LINC fellows” for 2024-25. The applicants are expected to have a 
research mentor in their home institution, who will provide a letter of support 
for their application. During the LINC fellowship year, the LINC fellows will 
remain in their current program/institution, and engage in a research project 
that can benefit from remote access to the data and computational resources of 
the LINC project, and collaboration with the LINC investigative team. For 
eligibility and application materials, please see:

https://connects.mgh.harvard.edu/outreach/

Thank you for sharing with any qualified applicants that you may know!

Anastasia.

| Anastasia Yendiki, Ph.D.
| Associate Professor, Harvard Medical School
| Associate Investigator, Massachusetts General Hospital
| 149 13th St. Suite 2301
| Charlestown, MA 02129
| Tel: 617-726-9434 | Fax: 617-726-7422
| Web: http://dmri.mgh.harvard.edu/a-y
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Re: [Freesurfer] License for FreeSurfer 5.x

[fsbuild]

External Email - Use Caution

Hello Rafa,
If you take a look under,
https://secure-web.cisco.com/1dfxSJC8JWSEz6n8dSa8oPi0pnwDlx9137h03BernH-2Q8eEewwiAs4_GzpGOKvQvQC3n0ZOzmkJywWiQhnZl1hp8X7dZz_1b5uzmyic7OwNcW2wT_tLTYBwTq7v44waYGSfLHYoIXzuMDkmGJA6TeCJ_9t27l3YBR-gpCXTlMtZF6idOKlosZWj2TboaTbNTa-2UVNDaP1QVnDMKL2k-1o-69Ad91inM7hvvpuulSQAEHZ1lC5a1j7TRDozna0YW0RVMmfzF2iGFstFaTgEkHv8sobpaqiseS6E2qOmt3jDk23FmAIoaOC5-ESz-TTffGyO92TI6lzK9RXiu4wG1ZQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0%2F
- you will see there is a Virtual Box ..vdi file for the 5.3.0 release,
https://secure-web.cisco.com/1RcGOCq2p6BYFO6rvNlcGnNuDdMKQaAC7luBVOPnx9yiqMFJA6ldXhzlTOSfcVrRQGXzGhINxzFYo_JFhUypqciLq0LT4ZY-Ej3rL9p3wkwBPeYEfHGq9AiHGiD2C0N98VtG4hc0VSzwpgRnRpJ6f9w-X4Xo1dSP2R3LnChQtmfool5KrHnUWDbLkb1vE0TFUS6fjdZ1tsu1z5xr1F2lavylYNlz2ZGk5HaShaPW2GiFl6LrnQs21aADXH1VPVwRm-kOwK06on5aY6IxxmAmgEFD3NCqLf7JJ1iNrGBd6YA5dWU-EDU6IjSiXqPepvPPlw0VeA5IOo6xGxQZmdvb8FA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0%2Ffreesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz
- but I think that Virtual Box image will be running CentOS6 (or some old 
version of CentOS). At that time we did not build or provide releases for 
Ubuntu linux. The version of CentOS in the VM and Ubuntu12 may use 
different versions of glibc so I’m not sure the packages with 5.3.0 binaries 
listed above will run on Ubuntu12.
We advertise the following caveat about switching to newer/different OS 
versions, or upgrading to a different (newer) Freesurfer release built with 
different compilers. Either of those changes will likely produce some 
difference in floating point math results.
Important Note:When processing a group of subjects for your study, it is 
essential to process all your subjects with the same version of FreeSurfer, on 
the same OS platform and vendor, and for safety, even the same version of the 
OS. While we continue to work to ensure that results match across platforms, 
there are none-the-less system-level libraries that are OS dependent. An 
exception to this rule is that you may view and edit files across any platform 
or version, and run some post-processing tools (outside the recon-all stream) 
if you check with us first (for instance you may run the longitudinal 
processing with newer versions).
But if it’s not an issue for you to run on an old version of CentOS instead of 
Ubuntu linux, then your best bet is to try and run the existing .vdi file 
listed above in the VirtualBox client - which you would need to download and 
install on your current Linux machine.
-R.
On May 30, 2024, at 12:34, Rafael Navarro rafa.navarr...@gmail.com 
wrote:External Email - Use 
CautionHello everyone,
I am working with a neuroimage model that uses the FreeSurfer 5.3 version as 
preprocessing (only autorecon-I). I have tried to install Freesurfer 5.3, but 
after reading previous messages in the mailing list It seems the license file 
format changed from FreeSurfer 5.3 to 6.0 due to an update of the 
Ubuntulibcrypt. Do you think that migrating the autorecon-I from v5.3 to 
v6.0 might affect the final results? Is there any alternative? Does a docker 
container running Ubuntu 12 with FreeSurfer 5.3 could work? Is still possible 
to get a license with the old format?
Regards!Rafa 
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[Freesurfer] License for FreeSurfer 5.x

[Rafael Navarro]

External Email - Use Caution

Hello everyone,

I am working with a neuroimage model that uses the FreeSurfer 5.3 version
as preprocessing (only autorecon-I). I have tried to install Freesurfer
5.3, but after reading previous messages in the mailing list It seems the
license file format changed from FreeSurfer 5.3 to 6.0 due to an update of
the Ubuntu libcrypt. Do you think that migrating the autorecon-I from v5.3
to v6.0 might affect the final results? Is there any alternative? Does a
docker container running Ubuntu 12 with FreeSurfer 5.3 could work? Is still
possible to get a license with the old format?

Regards!
Rafa Navarro
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Re: [Freesurfer] Recon-all for a common template

[Douglas N. Greve]

sounds like something is wrong with the image. Did you look at 
ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a 
head?

On 5/28/2024 6:07 AM, Chen Yang wrote:
>  External Email - Use Caution
>
> Hi everyone,
>
> I tried to run the reconstruction with the command line:  recon-all -i 
> ANTS_QS_template_MNI.nii.gz -subject CGBT -all
>
> then I got the error message:
> talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
> talairach_avi log file is transforms/talairach_avi.log...
> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
> Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 
> GNU/Linux
>
> And this is the error message in the talairach_avi.log:
> imgrege: no voxels in register
> ERROR: 'imgreg_4dfp 
> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305
>  
> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask
>  talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! 
> status=254
> ERROR: mpr2mni305 execution aborted
>
> Does anyone know how to solve this problem? Thanks so much!
>
> Best,
> Chen
> - Original Message -
>> From: "Chen Yang" 
>> To: "freesurfer" 
>> Sent: Monday, 20 May, 2024 13:59:13
>> Subject: [Freesurfer] Recon-all for a common template
>
>> External Email - Use Caution
>>
>> Dear Freesurfer Developers,
>>
>> my data is from 50 preschoolers and I created my own group template from 
>> these
>> kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti file
>> (see attached). Then we'd like to process this group template in Freesurfer 
>> to
>> reconstruct the cortical surfaces as the individual brain images. My question
>> is, how can i do the recon-all with the template? Because I only have this
>> template file I feel I don't have enough input files(?).
>>
>> Thanks in advance!
>>
>> Best regards,
>> Chen
>>
>> --
>> Chen Yang
>>
>> PhD Student
>> Independent Research Group 'Milestones of Early Childhood Development'
>> Max Planck Institute for Human Cognitive and Brain Sciences
>>
>> Email:ya...@cbs.mpg.de
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://secure-web.cisco.com/152_yjWgWiW7QaUCNWdHFdgPDgbGmCDd24wrNL32r-4bja7mb7PwZLrVrT8x_Ot8oLBlBDSrPO5K5UwFJww_c_Y6HNu9vVaziQgviXOWppVzFqlFYr7Go-t0P0ERBoTxsiCjkgkjp8sqNY12lF_6KIfy959AukP9K4eVWkLGWIlqP1lI_TQg2slA5qX1X8cEK857YHHC7vYcLM4qF7sKEU0nJ9xOLxq89J8jkqjRr9_G8fkxbUlriLEANx5HQWi_HJrmVUug78slky8NFQA8NxGyoQIVMsNUzUALsTUJfZAHI6rBpxPQLUejRDnI1ZFbAJwtYq_-f7tFE_dpFheFywA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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>> to
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>> 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.
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Re: [Freesurfer] SynthSR problem

[fsbuild]

External Email - Use Caution

Some commands such as mri_synthsr in previous releases, e.g., 7.4.1, use 
code built with Intel processor specific instructions that cannot run on an arm 
processor, i.e., there is not full backwards binary compatibility in that case 
using the Rosetta emulation environment on MacOS. Hence the “illegal 
instruction” error.
We do have a (more recent) development build on a Silicon Mac you can download 
via the link,
https://secure-web.cisco.com/1lWnZREm3JXXMeuMNsb_hOkyb2ipaBFlFN8u43RUzyQ6-cBpOY1HIvsCJ6Yq6EQh42_qmFVn3W8VSBrcGCmTg1ofVHbrA2XH36Cn4xi0k0HeHZVG0YnMoLQ3iwly-wQYbTnjuDPGI2_jkWwFekN96gabVpPg7pllxMYINHzHVpD4U0GWvGdRnvnpcF2h_20PzI5XZhR0U699zA75vyBnJ9JMLld3H6EOz4Da1ljgW2DZ4BTntHXXrwaxQGIKb20hYndKoBJXrJ5iMVGBQFIsS5ncHwrxaWBVUOxU0oVfR7vaKhPPuFTx8SKXbcUDiBX4ZlexIztClTwjKgklKIusnHA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg
 it has not yet gone the the same testing as done for a release. 
Please let us know if you run into issues trying it.
- R.

On May 28, 2024, at 16:08, Tabasi, Farhad farhad-tab...@uiowa.edu 
wrote:External Email - Use 
CautionHello FreeSurfer 
developers,
I am trying to use mri_synthsr to improve the quality of clinical scans, but 
this is the error I encountered:
Illegal instruction: 4
(I followed the instructions on SynthSR page, using mri_synthsr 
--iinput.nii--ooutput_synthT1.niicommand)
FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275OS: macOS 
Ventura (13.2.1) on iMac M1 (116 GB)
This is likely related to binary problems or CPU compatibility (especially with 
M1).Is there any solution to the issue?
Thanks,Farhad
Farhad Tabasi, MD(he/him/his)Postdoctoral ScholarHuman Brain Research Lab,
Department of Neurosurgery,
Carver College of Medicine,University of IowaCell: 
(858)588-2779___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] SynthSR problem

[Tabasi, Farhad]

External Email - Use Caution

Hello FreeSurfer developers,

I am trying to use mri_synthsr to improve the quality of clinical scans, but 
this is the error I encountered:

Illegal instruction: 4

(I followed the instructions on SynthSR page, using mri_synthsr --i input.nii 
--o output_synthT1.nii command)

FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275
OS: macOS Ventura (13.2.1) on iMac M1 (116 GB)

This is likely related to binary problems or CPU compatibility (especially with 
M1).
Is there any solution to the issue?

Thanks,
Farhad

Farhad Tabasi, MD (he/him/his)
Postdoctoral Scholar
Human Brain Research Lab,
Department of Neurosurgery,
Carver College of Medicine,
University of Iowa
Cell: (858)588-2779
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Re: [Freesurfer] Recon-all for a common template

[Chen Yang]

External Email - Use Caution

Hi everyone,

I tried to run the reconstruction with the command line:  recon-all -i 
ANTS_QS_template_MNI.nii.gz -subject CGBT -all

then I got the error message: 
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 
talairach_avi log file is transforms/talairach_avi.log...
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 
GNU/Linux

And this is the error message in the talairach_avi.log:
imgrege: no voxels in register
ERROR: 'imgreg_4dfp 
/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305
 
/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask
 talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! 
status=254
ERROR: mpr2mni305 execution aborted

Does anyone know how to solve this problem? Thanks so much!

Best,
Chen
- Original Message -
> From: "Chen Yang" 
> To: "freesurfer" 
> Sent: Monday, 20 May, 2024 13:59:13
> Subject: [Freesurfer] Recon-all for a common template


> External Email - Use Caution
> 
> Dear Freesurfer Developers,
> 
> my data is from 50 preschoolers and I created my own group template from these
> kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti file
> (see attached). Then we'd like to process this group template in Freesurfer to
> reconstruct the cortical surfaces as the individual brain images. My question
> is, how can i do the recon-all with the template? Because I only have this
> template file I feel I don't have enough input files(?).
> 
> Thanks in advance!
> 
> Best regards,
> Chen
> 
> --
> Chen Yang
> 
> PhD Student
> Independent Research Group 'Milestones of Early Childhood Development'
> Max Planck Institute for Human Cognitive and Brain Sciences
> 
> Email:ya...@cbs.mpg.de
> 
> ___
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> 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.

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Re: [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar

[fsbuild]

External Email - Use Caution

If you still have the VM setup on your machine, you 
can open a new terminal window and then you should see the Freesurfer 
Environment is setup,

  

FREESURFER_HOME /home/developer/7.2.0/dev

FSFAST_HOME /home/developer/7.2.0/dev/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR 
/home/developerfreesurfer/7.2.0/subjects

MNI_DIR 
/home/developer/7.2.0/mni

garnet2[0]:tmp$ ls $FREESURFER_HOME/bin/aparc*

  

The aparc* and aseg* commands should all be in your path, i.e.

  

$ which aparc_stats_aseg

/home/developer/7.2.0/bin/aparc_stats_aseg

  

$ which aparcstats2table

/home/developer/7.2.0/bin/aparcstats2table

  

$ which aparcstatsdiff

/home/developer/7.2.0/bin/aparcstatsdiff

  

$ which aparc2feat

/home/developer/7.2.0/bin/aparc2feat

  

$ which aseg2feat

/home/developer/7.2.0//bin/aseg2feat

  

$ which asegstats2table

/home/developer/7.2.0//bin/asegstats2table

  

$ which asegstatsdiff

/home/developer/7.2.0//bin/asegstatsdiff

  

You should be able to get some info about the commands using the "-h" or help 
option.

  

garnet2[0]:tmp$ aparcstats2table -h

Usage: 

Converts a cortical stats file created by recon-all and or

mris_anatomical_stats (eg, ?h.aparc.stats) into a table in which

each line is a subject and each column is a parcellation. By

default, the values are the area of the parcellation in mm2. The ...

. rest of output deleted 

  

- R.

  



On 5/21/24 07:45, Carina Obermüller (carina.obermuel...@live.at) wrote:



  External Email - Use Caution

Dear Freesurfer team,

I am looking for a group stats command like the asegstats2table and 
aparcstats2table command for hipposubfields, brainstem and amygdalar, but I 
couldn’t find it in the archives. I remember it was mentioned in the recent 
Freesurfer course, but I can’t find it anymore. Could you help me out?
Also more generally, is there an overview page of all the possible group stats 
commands?

Thank you so much in advance for your reply!

Sincerely,

Carina


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Re: [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar

[Carina Obermüller]

External Email - Use Caution

Dear Antoine,

Thank you so much again for your reply! I did as you said and it seems like the 
script is on my computer now, but I get this error:


Could not find hipposubfields.rh.T1.v22.txt, skipping subject.


For all files. The first few lines looked like this:


carinaobermuller@MBP-di-Carina raw_data_freesurfer_Dec2023 % 
ConcatenateSubregionsResults.sh -f amygdalar-nuclei.lh.T1.v22.txt -f 
amygdalar-nuclei.rh.T1.v22.txt -f brainstem.v13.txt -f 
hipposubfields.lh.T1.v22.txt -f hipposubfields.rh.T1.v22.txt -s $PWD

cmd: /Applications/freesurfer/7.4.1/bin/ConcatenateSubregionsResults.sh -f 
amygdalar-nuclei.lh.T1.v22.txt -f amygdalar-nuclei.rh.T1.v22.txt -f 
brainstem.v13.txt -f hipposubfields.lh.T1.v22.txt -f 
hipposubfields.rh.T1.v22.txt -s 
/Users/carinaobermuller/Documents/raw_data_freesurfer_Dec2023

Gathering results from:

/Users/carinaobermuller/Documents/raw_data_freesurfer_Dec2023

Looking at files:

amygdalar-nuclei.lh.T1.v22.txt amygdalar-nuclei.rh.T1.v22.txt brainstem.v13.txt 
hipposubfields.lh.T1.v22.txt hipposubfields.rh.T1.v22.txt

Outputting results to:

/Users/carinaobermuller/Documents/raw_data_freesurfer_Dec2023


Concatenating stats for file: amygdalar-nuclei.lh.T1.v22.txt

Will write results to: amygdalar-nuclei.lh.T1.v22_concat.txt

Working on subject: Raw_TP1

Could not find amygdalar-nuclei.lh.T1.v22.txt, skipping subject.


Working on subject: Raw_TP2

Could not find amygdalar-nuclei.lh.T1.v22.txt, skipping subject.


Working on subject: T1w_AoC1001_T1_reor

Could not find amygdalar-nuclei.lh.T1.v22.txt, skipping subject.


Working on subject: T1w_AoC1001_T2_reor

Could not find amygdalar-nuclei.lh.T1.v22.txt, skipping subject.



The files are in the “stats” folder of each subject folder. I am wondering if 
the script is calling the files from a different folder? Or am I doing 
something else wrong?


Best wishes


Carina

Il giorno 24 mag 2024, alle ore 11:54, COSSA ANTOINE IDRS 
 ha scritto:

Dear Carina,

I got the same problem at first, I thought it was coming from my computer. To 
resolve this, I simply downloaded the missing script file from 
here:https://secure-web.cisco.com/1P3_VeR3p4seMFU_4h_YDuZEeXwHEzHxThUx__-6Wf-M_OFWQqKTmTvHp71RI2elBqtTkbha89oeZVXhcpZANP9sHGVb4WLtmqqln-VZmQSQISaL_4G5Amhxs9aGiGZfyiAAASILFpth0Y6PVjHHSjwhV7SaEdnqWlPw3TkaHpMix5_7nm22xxrGoiIOcPbeqdDGqWsiNzoof6XNs2o1ulTNsShK2sf-_zEXBxCN4rmiv-MsCFiKlPZlK_5zoaLyU4BMVGv8_fB1GcZ8-wuOUKC-T9oVMAVMVJHgh5xI1l8706QZpBmISLBzgCr6AZfmd/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fftp%2Fdist%2Ffreesurfer%2Fdev_binaries%2Fcentos7_x86_64%2FConcatenateSubregionsResults.sh,
put it in the bin folder of FreeSurfer and rerun the source command (source 
$FREESURFER_HOME/SetUpFreeSurfer.sh).
This should fix your issue.

Kind regards,
Antoine


De : Carina Obermüller 
mailto:carina.obermuel...@live.at>>
Envoyé : jeudi 23 mai 2024 17:01
À : COSSA ANTOINE IDRS 
mailto:antoine.co...@servier.com>>
Cc : Carina Obermüller 
mailto:carina.obermuel...@live.at>>
Objet : Re: Group Stats for hipposubfields, brainstem and amygdalar

CAUTION: This email originated from outside the company.
Dear Antoine,

Thank you so much for your quick reply 

I ran this command in the directory that contains the free surfer file 
structure of my data, but it showed me that the command doesn’t exist:

ConcatenateSubregionsResults.sh -f amygdalar-nuclei.lh.T1.v22.stats -f 
amygdalar-nuclei.rh.T1.v22.stats -f brainstem.v13.stats -f 
hipposubfields.lh.T1.v22.stats -f hipposubfields.rh.T1.v22.stats -s $PWD

Do you know where I am going wrong here?

Kind regards
Carina


Il giorno 22 mag 2024, alle ore 16:36, COSSA ANTOINE IDRS 
 ha scritto:

Dear Carina,

I think you can refer to this page : ConcatenateSubregionsResults - Free Surfer 
Wiki 
(harvard.edu)
 and use the ConcatenateSubregionsResults.sh command 

Kind regards,
Antoine

De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Carina Obermüller 
mailto:carina.obermuel...@live.at>>
Envoyé : mardi 21 mai 2024 13:45
À : freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc : Carina Obermüller 
mailto:carina.obermuel...@live.at>>
Objet : [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar

CAUTION: This email originated from outside the company.

External Email - Use Caution

Dear 

[Freesurfer] freesurfer coordinate systems error: mismatch region hippocampal atlas in matlab and freeview for high resolution

[Le, Jarod]

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to acquire the hippocampal subfields and nuclei of the amygdala 
using a high resolution of 0.333 mm3. However, when comparing the results of 
using the Freesurfer Coordinate System in matlab, using the reported tkrRAS to 
VoxCRS equation, and the results of Freeview, by manually inputting the tkrRAS, 
they report different subfields. We were wondering whether this the matlab 
coordinate system is getting rid of information or the freeview is adding 
information? How could get more precise information with the matlab coordinate 
system?

When looking closely, it appears that VoxCRS coordinates can have multiple 
subfields within the same integer by slightly altering the tkrRAS coordinates 
and noticing the subfield region name change using freeview.

For example, we have a tkrRAS coordinate of [-24.65, -7.82, -21.04].
Putting this coordinate into freeview it gives us an "Unknown" region.
Using the matlab coordinate system, we first transform the tkrRAS coordinates 
into the high resolution tkrRAS coordinates due to the mismatch of volume 
between the lower and high resolution. Then we use, VoxCRS = inv(Torig)*[tkrR 
tkrA tkrS 1]' to get the VoxCRS and then check the volume to get the subregion. 
It gives us a "CA1" region.

I have searched the archive of past problems. However, no similar problems have 
reported.

Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-V6.0.02beb96c
Freeview Version: Version 2.0 Build Jan 18 2017 16:48:55
MATLAB Version: R2018b
Ubuntu Version: 18.04.4

Freesurfer Coordinate System link: 
https://secure-web.cisco.com/1a-L_exiDRUdrPGFnZvtMx-VhHRhWEfIDjmkx_H9zNuPhjNrW8-tM1p4TUNbGRGfizhMmwSjWBLEhcdLmgpDgawRXhV7qtbzzJlREUFhManFIzXldzLBP5j3wnPCsIqwcKJWBTut3td_uLvK4_hwFFcBQj75nCLngPFDm4uScJZCfvbgGCW4i_yC-UPpXwbk9jI_rb6Dy5Q8uG2mb-4tR_mVHNb9YkqOTAmlWM8XgScjVrKRhulsljrK1rfRVihM5v_V08wZOUIKA9XYFAH6EaBbrVr5VHm4vPYjPuosM7WUaQcpoX0pRIcyQyFRA0c2Cgfrlf3t_nCS30Ml2MXFLIA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCoordinateSystems
Segmentation of hippocampal subfields and nuclei of the amygdala link: 
https://secure-web.cisco.com/1f_b9T_6PJ49eQDQwBXq2S2L2mj5oSdjOEWB7Fjc78JCCPEJK3QmKLFv9OHMh3BRYY8UnbrBniAMstAqxh--LEEEiqd-03OepH9avegi-ceRR_OCDEuyJD5KU-QWD18ewO6FpsCE049t4490FHXgXwWPdIeyKMKItghzMgPEp3FZN6UmD91hpBxUyxy6TWaxRCPK0ImiQ73H52uXYvdBQ_F0oIYK8SF5xyoldq2uyj2fH8JSVOztQKJObdtxirljcK_C4rOIzPwmgQUssQwi2jeLiM663MZNLvQ-iVMdd_hlVETCdi3J3oReSBqOily9xZn3K5sWCTss8-BSNLGAWhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala

Sincerely,
Jarod

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Re: [Freesurfer] MAC compatibilty

[fsbuild]

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The Intel binaries should still run on Silicon Macs using the built-in 
Rosetta emulation environment. So if you want to use an official release, 
then the Intel binaries from the most recent June 2023 7.4.1 release can be 
found here:
https://secure-web.cisco.com/1PlXQxoEX-x05USM5h21mbTgkWDKGf26NwLJXc-0TKpfOiCFIPKTNfixRTstm4lwdFle1ckZQaNDG9K2uXTrL4PgECdRb1kB_7yoS7khQb0ehN9jhQdUEx760OIsW4yS15fGVX2egl-kP-gUfA8mcGgT60fYkpOBtL34Q4XfiQpnY1cyK4Qqix_1L2MqBZwQmqpy77YwZet2977GkKZQWCJJH3Efq_fu4bs31PqnDT7GH0wKw4xpynQgYZqKFDx2AkPPLgjGxEE4pw0Wi67HAZl4XlGt1_52MXZDtYFdwJ-LmwkxE_VdxXa68ba42bxgnpVTNDrEMR3T3qZGRJ5NzYw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
There is however a newer development (non-release) build compiled natively for 
the Silicon (arm64) Macs. You can find development builds under,
https://secure-web.cisco.com/1bqoWa8LCXJXDBOMIgjvymagPdUuAoVFBzhDkQcCJ8BO0z-AZtSuIBxg3dgBxnDm_R3YCWCP73q0CQsSKFyW2x74gcZTMU-skv2NKEJpxs8JrKVEBT9cduIT3bgaeRqTaKYbAPkmyixKaV3b5DspaTK1FKHuF3XoG-_UI7jDI2Wlh7nRboHjFUkY65GZX8wF1RiHq8O6Lma-thaFJNoIPCW47mSNy_k8BfzB06E6t9dnJ2ebKfeuJvhvRc2jgf4x-yYmD6Q3l6kpMd0APnM1cXP-hxyldsY86BJmBjC1agSZGZgW3NFrcB3Sh836GHFxKKixmeiyxw8GocHHyif1H3A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev
- and the current arm64 .pkg file installer is:

https://secure-web.cisco.com/1v7jUCTarAa0YZGcgQjK2FDqKV6MOl2jENY0Cmgh3LS7Tbjl3BBwYxUBU9KrYpFUz3kNsQXeNAsuR87a0V4E9JSverkt5GYgtXxTTr6_bL8FBO9kdzQ99iyRTfPKFsLSMXBpJ4maosVp3cAWGAFzfc4nWl-dxrxBTSHHomvryS8Vyq0T4byXQRjA_3hAvxNL2-uHTW4X4q4Cf89AxweyE8ewSJ9IZUQen4XPJAmNuVMZhYrQIP2iPIgateMIe6ARMmsEORI-tXGrYBL8Hq83RiW-3YwQ7kDJl0sbadpIsRabO9xxP6FCfjbSv4odPFCdyucnownn7fGoh9s7c_EGhyw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg
- R.

On May 25, 2024, at 04:58, Silvia Montanari silymontanar...@yahoo..it 
wrote:External Email - Use Caution 


Good morning, my office needs to buy a new computer and it’s mandatory that it 
can run free surfer properly. I couldn’t really find definitive informations 
about the compatibility with latest Mac machines with M2-M2pro-M3 processors. 
Since I always had Intel, can you help understand which Mac it’s better to have 
in order to not have problems with freesurfer?

Thank you in advance,
Silvia Montanari

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[Freesurfer] MAC compatibilty

[Silvia Montanari]

External Email - Use Caution

Good morning, my office needs to buy a new computer and it’s mandatory that it 
can run free surfer properly. I couldn’t really find definitive informations 
about the compatibility with latest Mac machines with M2-M2pro-M3 processors. 
Since I always had Intel, can you help understand which Mac it’s better to have 
in order to not have problems with freesurfer? 

Thank you in advance,
Silvia Montanari

___
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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. 

[Freesurfer] Research Technician positions in the FreeSurfer lab

[Player, Allison A. Stevens]

Hi everyone,
If you or anyone you know is looking for entry-level Research Technician 
positions working with FreeSurfer and/or postmortem human brain MRI research, 
please feel free to check out or share some of the job openings in our lab:

https://lcn.martinos.org/jobs/

We are also looking for more experienced individuals who are interested in lab 
management. Feel free to contact me (best to do with your resume attached)!

Allison Stevens
Lab Manager
Lab for Computational Neuroimaging, FreeSurfer Development Team
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Charlestown, MA



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 .
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. 

[Freesurfer] squirrel data sharing format available in beta

[Gregory Book]

External Email - Use Caution

The squirrel data sharing format is now available in beta format and we're
looking for public comment. The squirrel format is designed to use the
minimum number of objects to describe all parts of neuroimaging analysis.
From experiments and raw data to analysis methods and results, all
information can be categorized into 10 object types. Using a
hierarchical storage, the format can store any number of subjects, any
number of imaging sessions, any number of visits, and any modality of data.
It handles not just imaging data, but demographics, measures, vitals, and
drugs.

Simple to use, simple to share.
* convert from DICOM to squirrel
* convert from BIDS to squirrel
* modify existing packages
* packages are in 7zip format, and JSON is human readable
* available for RHEL8, RHEL9, and Debian12/Ubuntu22

The squirrel utilities are in beta, so not all parts work, but we're
looking for testers and feedback!

Download the squirrel utils from 
https://secure-web.cisco.com/1WRNkvQPK4BOcCo4fgUYLyLTBlLdPW7fwixbJiXy16MAKLgW3vnRY88djSv8H3AqH0gZVy-pzMUEyuPetB0N5Oaep_D-NWZAj8VucoVvxwpwOzyRV-s8PNAZ2vOcKM2kBI4we1pf9dCtrikVem_lXGJ1sgGJzvdzcr8rIL1dhNWeDil6oYvXOp4nUROsrmTsRxvkssv33mnQPdh3Vwr-rwlc5Lwtzi8UvD22-77WDge9qDmVD7IAH1XnQtjhDrB8SYu8lhbxceEcMwSTyIgPcZenfSSKYzbwSiO3yjoVzFL68HZ1Jaj4WXEXw_5MJI3JHNhF2OL-I1Wo9koTjSoox8g/https%3A%2F%2Fgithub.com%2Fgbook%2Fsquirrel%2Freleases
Documentation and the squirrel specification:
https://secure-web.cisco.com/1uAU1-QCnkUDsyb1PHsY1vqWB553FNwLN1raYY7xR1zBejLyjEw2NI4mS72nELnQg7JTBKhTPOkat4vugEaOaC1pL7IYxb1u2yDZReVeHk7jk5rPFowK4WTXAB_46YIjS9lRlhfkm4DLr1juxP1BNUR7HaIQ2ehNhrrvP0VTTOYoRiTfIEggOUJXH89tWGq0z0KNUQBi9yrVfyeVSHvMK15ho5H1195UbWADJTxrcVEsgtYoTT4EK6-fcJZwDvueVO2NnQTrjUIyIO4b87BZZ7Vx3K5SNdI94t9aJQwXKh-AB077QLdb4LranOpQCBBr7/https%3A%2F%2Fdocs.neuroinfodb.org%2Fnidb%2Fcontribute%2Fsquirrel-data-sharing-format%2Fsquirrel-utilities
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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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. 

[Freesurfer] run_samseg: Optimizer: maximalDeformation is too small; stopping; killed

[Stefano Cerri]

External Email - Use Caution

Hi Marie,


The error message "Killed" is usually thrown when the device runs out of
memory. Can you double-check that this is not the case? If you're on Ubuntu
you can track your memory usage with the command ("htop" or "top").


The SAMSEG log you provided looks good to me.


Stefano


[Freesurfer] run_samseg: Optimizer: maximalDeformation is too small;
stopping; killed


Ringki Marie Siewert

 Wed, 22 May 2024 11:04:52 -0700


External Email - Use Caution

Hello Freesurfer Developers,

I'm a medical student training with Freesurfer for my doctor thesis. My
goal is to measure the brain volumetry of patients via SAMSEG. Attached is
my logfile for run_samseg.


When i run the samseg command:


run_samseg --input STRUCT_samseg.nii.gz --output
~/fsl_course_data/registrat/SamsegOutput --threads 3



where: STRUCT_samseg.nii.gz is a T1 w image of a normal human brain.





It runs for a while an then gives me the message:



*Optimizer: maximalDeformation is too small; stopping*

*iterationNumber: 0*

*Killed*

and just stops. There the files created as samseg output:

samseg.talairach.lta  template_coregistered.mgz
cost.txt  template.lta  template_transforms.mat,



 but not the stats file that estimates the volumetry of the brain.

I've searched the forum but there weren't any similiar reports for this
error.



1) FreeSurfer
version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460

2) Plattform: Ubuntu 20.04.6 LTS

3) uname -a: Linux TABLET-TSKI5C88 5.15.146.1-microsoft-standard-WSL2 #1
SMP Thu Jan 11 04:09:03 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

4) log as text file is attached



Last but not least I want to thank you for all your hard work!

I really appreciate all the advice and support you give.





Have a nice day,



Marie

Script started on 2024-05-22 15:06:09+02:00 [TERM="xterm-256color"
TTY="/dev/pts/0" COLUMNS="72" LINES="46"]
 freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/7.4.1
FSFAST_HOME   /usr/local/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/7.4.1/subjects
MNI_DIR   /usr/local/freesurfer/7.4.1/mni
FSL_DIR   /home/ringki/fsl

 ]0;ringki@TABLET-TSKI5C88: ~/fsl_course_data/registration/SamsegOutput
 [01;32mringki@TABLET-TSKI5C88 [00m:
[01;34m~/fsl_course_data/registration/SamsegOutput [00m$
 run_samseg --input STRUCT_samseg.nii.gz --output
~/fsl_course_data/registration/
 [A [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C
[C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C
[C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C
[C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C
[C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C
[C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C
[C [C [C [C [C [C [C [C [C [C

SamsegOutput --threads 3
##--
  Samsegment Options
##--
output directory: /home/ringki/fsl_course_data/registration/SamsegOutput
input images: STRUCT_samseg.nii.gz
modelSpecifications: {'FreeSurferLabels': [0, 165, 258, 16, 24, 

[Freesurfer] run_samseg: Optimizer: maximalDeformation is too small; stopping; killed

[Ringki Marie Siewert]

External Email - Use CautionHello Freesurfer Developers, 

 

I'm a medical student training with Freesurfer for my doctor thesis. My goal is to measure the brain volumetry of patients via SAMSEG. Attached is my logfile for run_samseg. 

 

 

When i run the samseg command: 

 


run_samseg --input STRUCT_samseg.nii.gz --output ~/fsl_course_data/registrat/SamsegOutput --threads 3

 

where: STRUCT_samseg.nii.gz is a T1 w image of a normal human brain.

 

 

It runs for a while an then gives me the message: 

 

Optimizer: maximalDeformation is too small; stopping

iterationNumber: 0

Killed

and just stops. There the files created as samseg output: 

samseg.talairach.lta  template_coregistered.mgz
cost.txt              template.lta          template_transforms.mat, 

 

 but not the stats file that estimates the volumetry of the brain. 

I've searched the forum but there weren't any similiar reports for this error. 

 

1) FreeSurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460

2) Plattform: Ubuntu 20.04.6 LTS 

3) uname -a: Linux TABLET-TSKI5C88 5.15.146.1-microsoft-standard-WSL2 #1 SMP Thu Jan 11 04:09:03 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

4) log as text file is attached 

 

Last but not least I want to thank you for all your hard work! 

I really appreciate all the advice and support you give. 

 

 

Have a nice day, 

 

Marie  
Script started on 2024-05-22 15:06:09+02:00 [TERM="xterm-256color" 
TTY="/dev/pts/0" COLUMNS="72" LINES="46"]
 freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/7.4.1
FSFAST_HOME   /usr/local/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/7.4.1/subjects
MNI_DIR   /usr/local/freesurfer/7.4.1/mni
FSL_DIR   /home/ringki/fsl


]0;ringki@TABLET-TSKI5C88: ~/fsl_course_data/registration/SamsegOutput 
ringki@TABLET-TSKI5C88:~/fsl_course_data/registration/SamsegOutput$
 run_samseg --input STRUCT_samseg.nii.gz --output 
~/fsl_course_data/registration/ 


SamsegOutput --threads 3
##--
  Samsegment Options
##--
output directory: /home/ringki/fsl_course_data/registration/SamsegOutput
input images: STRUCT_samseg.nii.gz
modelSpecifications: {'FreeSurferLabels': [0, 165, 258, 16, 24, 8, 47, 15, 259, 
3, 42, 7, 46, 41, 2, 63, 54, 18, 53, 44, 17, 31, 5, 85, 60, 28, 14, 26, 12, 51, 
62, 58, 77, 4, 30, 43, 52, 11, 49, 13, 50, 10, 80, 72], 'atlasFileName': 
'/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz',
 'names': ['Unknown', 'Skull', 'Soft_Nonbrain_Tissue', 'Brain-Stem', 'CSF', 
'Left-Cerebellum-Cortex', 'Right-Cerebellum-Cortex', '4th-Ventricle', 
'Fluid_Inside_Eyes', 'Left-Cerebral-Cortex', 'Right-Cerebral-Cortex', 
'Left-Cerebellum-White-Matter', 'Right-Cerebellum-White-Matter', 
'Right-Cerebral-White-Matter', 'Left-Cerebral-White-Matter', 
'Right-choroid-plexus', 'Right-Amygdala', 'Left-Amygdala', 'Right-Hippocampus', 
'Right-Inf-Lat-Vent', 'Left-Hippocampus', 'Left-choroid-plexus', 
'Left-Inf-Lat-Vent', 'Optic-Chiasm', 'Right-VentralDC', 'Left-VentralDC', 
'3rd-Ventricle', 'Left-Accumbens-area', 'Left-Putamen', 'Right-Putamen', 
'Right-vessel', 'Right-Accumbens-area', 'WM-hypointensities', 
'Left-Lateral-Ventricle', 'Left-vessel', 'Right-Lateral-Ventricle', 
'Right-Pallidum', 'Left-Caudate', 'Right-Thalamus', 'Left-Pallidum', 
'Right-Caudate', 'Left-Thalamus', 'non-WM-hypointensities', '5th-Ventricle'], 
'colors': [[0, 0, 0, 0], [255, 165, 0, 255], [128, 128, 128, 255], [119, 159, 
176, 255], [60, 60, 60, 255], [230, 148, 34, 255], [230, 148, 34, 255], [42, 
204, 164, 255], [128, 0, 128, 255], [205, 62, 78, 255], [205, 62, 78, 255], 
[220, 248, 164, 255], [220, 248, 164, 255], [0, 225, 0, 255], [245, 245, 245, 
255], [0, 200, 221, 255], [103, 255, 255, 255], [103, 255, 255, 255], [220, 
216, 20, 255], [196, 58, 250, 255], [220, 216, 20, 255], [0, 200, 200, 255], 
[196, 58, 250, 255], [234, 169, 30, 255], [165, 42, 42, 255], [165, 42, 42, 
255], [204, 182, 142, 255], [255, 165, 0, 255], [236, 13, 176, 255], [236, 13, 
176, 255], [160, 32, 240, 255], [255, 165, 0, 255], [200, 70, 255, 255], [120, 
18, 134, 255], [160, 32, 240, 255], [120, 18, 134, 255], [13, 48, 255, 255], 
[122, 186, 220, 255], [0, 118, 14, 255], [12, 48, 255, 255], [122, 186, 

[Freesurfer] Fwd: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus

[Ahsan Ali]

External Email - Use Caution

Hello everyone,

Could anyone please help me to know which Atlas is used in the segmentation
of corpus callosum, hippocampus, and fornix using freeSurfer from Brian MR
images. I have gone through the literature but couldn't find it.

With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics (Biomedical Engineering Group)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552

-- Forwarded message -
From: Fischl, Bruce R.,PHD 
Date: Wed, May 22, 2024, 10:52 PM
Subject: RE: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus
Callosum, Hippocampus
To: Ahsan Ali 


Can you please post to the list so that others can answer?



*From:* Ahsan Ali 
*Sent:* Wednesday, May 22, 2024 1:04 PM
*To:* Fischl, Bruce R.,PHD 
*Subject:* Re: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus
Callosum, Hippocampus



*External Email - Use Caution*

Dear sir,



It is not clear from these papers to me.



With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics (Biomedical Engineering Group)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552



On Wed, May 22, 2024, 8:19 PM Fischl, Bruce R.,PHD 
wrote:

Mostly these:



https://secure-web.cisco.com/1DKaAagv5wrZcn_HucsSWH8TG1zknHKvHLkGgJhoy1pwq5h5Gy44-n3iYuTFbU_IjGt0vWiNR5NG5XUSF6Q86czJMoJRU0GQjjHxn1JLn23qbq8MvFW4_ghw2XFXMtfI-eVfZKljxj-ITwDft1q3zamXDRxoqvtVjobVOc38fJ8jiQ-rMfBSME1Fd6s-JihLgk5Ce-PUNTmh2x8QhuXpIFDOZ7Ob6S_nzRnFJEli7zUouGvihFDaMjgZgwemDtvJYDkt2VtJ4teOYPxp0K8wVYeMBKWgaGggZAgMAepMQgJT_HVq57ig8bJF9mafB3-AVbgHynMDW-WfxgRdqSAL1-A/https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F15501102%2F


https://secure-web.cisco.com/1XuxKv5CEuHRfXAdPzciFLM-HiNv8hX8h1hN2vYlGz0J9uz79NMgzaagVvButgJoxFDkR-H-CJv1KSQY8x3C_ddrl7Cq7SjoKAFNvx9gRCIbcYwGpsjlOwC_s6rSgvtGUQlXc42701tL_kY8uM6THlNnJ6A2xmfWKOxL6Dwhjk8PW-A7jHqpunbBkm--S533jTawiFOd_XS6mZYORq7q3eOaUjx57irYEbluTAkAUwi_KucSWnQK4bwZrUyvv-SvCMO-ONY2flGkql0hkSP32ZPpfSO53UHIOU5r8-xd5XkHGYVOoMhAPT9mle8XCEoWTVveyaWSxhSMmA6sKq9MXMw/https%3A%2F%2Fdoi.org%2F10.1016%2FS0896-6273%2802%2900569-X




cheers

Bruce

*From:* Ahsan Ali 
*Sent:* Wednesday, May 22, 2024 4:31 AM
*To:* Freesurfer support list ; Huang,
Yujing ; Fischl, Bruce R.,PHD <
bfis...@mgh.harvard.edu>
*Subject:* Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus
Callosum, Hippocampus



*External Email - Use Caution*

Dear FreeSurfer Team,

After reviewing the literature, I have a question: which atlases are used
in the segmentation of the fornix, corpus callosum, and hippocampus from
magnetic resonance images using FreeSurfer? This is a significant question
for me, and I would appreciate a clear and concise answer. Please provide
some relevant references.




With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics and Biomedical Engineering (AMBE)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552

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[Freesurfer] Intensity affected after using -c flag in mri_convert

[ERNEST KISSI]

External Email - Use Caution

Dear fresurfer team,

Why does the use of conform flag (-c) in mri_convert affect the intensity
of the image?   I have an image with absolute intensity of 1000 and after
using the conform flag in mri_convert, the intensity is around 98.1. why is
there a different scale in the intensity after the use of the flag?
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Re: [Freesurfer] Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus

[Fischl, Bruce R.,PHD]

Mostly these:

https://pubmed.ncbi.nlm.nih.gov/15501102/
https://doi.org/10.1016/S0896-6273(02)00569-X

cheers
Bruce
From: Ahsan Ali 
Sent: Wednesday, May 22, 2024 4:31 AM
To: Freesurfer support list ; Huang, Yujing 
; Fischl, Bruce R.,PHD 
Subject: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, 
Hippocampus


External Email - Use Caution
Dear FreeSurfer Team,

After reviewing the literature, I have a question: which atlases are used in 
the segmentation of the fornix, corpus callosum, and hippocampus from magnetic 
resonance images using FreeSurfer? This is a significant question for me, and I 
would appreciate a clear and concise answer. Please provide some relevant 
references.


With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics and Biomedical Engineering (AMBE)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552
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Re: [Freesurfer] fspalm error

[Stefano Delli Pizzi]

External Email - Use Caution

I have the same error that doesn't resolve with --mgh or mgz. 

warning: excluding contrast file 
/Volumes/mnu/MRI/XXX/NIFTI/FreeSurfer/rs-fMRI_AROMA/G3V0_Comparison/fc.MDseed.surf.rh/MD/G3V0_PALM.glmdir/group.effect/C.dat
 since it has multiple rows
ERROR: for surface based analysis, input cannot be nii or nii.gz

Thanks

Stefano

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[Freesurfer] Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus

[Ahsan Ali]

External Email - Use Caution

Dear FreeSurfer Team,

After reviewing the literature, I have a question: which atlases are used
in the segmentation of the fornix, corpus callosum, and hippocampus from
magnetic resonance images using FreeSurfer? This is a significant question
for me, and I would appreciate a clear and concise answer. Please provide
some relevant references.


With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics and Biomedical Engineering (AMBE)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552
___
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[Freesurfer] PhD candidate position - high-resolution imaging of the human claustrum

[Zaretskaya, Natalia (natalia.zaretsk...@uni-graz.at)]

External Email - Use Caution

Dear colleagues,

I would greatly appreciate if you could forward this job announcement to 
potentially interested candidates.

The Visual Neuroscience Lab (PI: Natalia Zaretskaya) at the Institute of 
Psychology, University of Graz jointly with the fMRI Lab (PI: Christian 
Windischberger) at MR Center of Excellence, Medical University of Vienna are 
looking for a doctoral candidate to join us in the project dedicated to 
high-resolution imaging of the human claustrum, one of the most mysterious and 
least studied areas of the human brain. You will join the Vienna-based part of 
the team and will be involved in piloting and conducting experiments using 7 
Tesla MRI.

You will find further details and the official job advertisement text below.

---

Visual Neuroscience Lab (PI: Natalia Zaretskaya) at the Institute of 
Psychology, University of Graz jointly with the fMRI Lab (PI: Christian 
Windischberger) at MR Center of Excellence, Medical University of Vienna is 
looking for a


Doctoral Candidate
within the framework of the FWF funded project
"High-resolution imaging of the human claustrum"
(Project-Assistant; 30 hours a week; fixed-term employment initially for 1 year 
with a possibility of extension for up to 4 years in total)

Project description
The project is dedicated to investigating the claustrum, one of the most 
mysterious structures of the human brain. It is led by the PI Natalia 
Zaretskaya in Graz and the co-PI Christian Windischberger in Vienna. You will 
join the Vienna-based part of the team and will be involved in piloting and 
conducting experiments using 7 Tesla MRI. Project-related publications:


* Adam Coates, Natalia Zaretskaya, High-resolution dataset of manual 
claustrum segmentation, Data in Brief, Volume 54, 2024, 
https://secure-web.cisco.com/1zeq_ipnEfhXQWA1cKbf1_H6iUzhhXoee44VMGbemOb2mpolleFtctEW4DwEb-StQZTZFoWS1kQ9yodV6lGO_Mroe5-LIkd8XTAEVb5vzum9xJhlyxsUgcTMy_VxST4YEOiDyal4GnVEfdAhMahWS0rFpGhHWxckTKTXeDJ8Mf7H0bY-Y2ozjHzS0EAZKCWMBJEutQsMPpbocIyxmexAocpMa-ogY5IX6Dno45ZuZSRMh0V-vN5C83AoTPeuYTjdnn9sdanYlaqXeJtEaoKd5ii6tWdSyI3ZJzi6PvFRQjSf6JQWdr-vbZBVNPk89xAyT/https%3A%2F%2Fdoi.org%2F10.1016%2Fj.dib.2024.110253

* Adam Coates, David Linhardt, Christian Windischberger, Anja 
Ischebeck, Natalia Zaretskaya, High-resolution 7T fMRI reveals the visual 
sensory zone of the human claustrum, bioRxiv 2023.09.18.558213; 
https://secure-web.cisco.com/1XoozScW5lqeJFO6PKFmaXkaXPux1aUn48UIO7n1abH2yi_CiipN9I0NHY3-mS5HlfnioYKjBj0JJBdPMuVozTXHUt9H7vrnwY9awY3IGWKDiandr0eqCCKMwhbi_e5ise-tB4cZmNgVNa-g7Xq8c36PE0oMsjrHNsubfLDUJ56EHHBzKugOgOoywUZHdaLhF9e-Dbyg1oMdr8uSK_SNziLSi9YnroXlce9uJIvEpvDcabMDtAAvPYJsljW0pMDRzBf_KNjUKkdMXGobTr8W6TLfZ6QTyuPTdQxBZQ7rdFqDHfLRRWiGyqp4SzMdkeFrK/https%3A%2F%2Fdoi.org%2F10.1101%2F2023.09.18.558213



Your duties

* Participation in planning, preparing and conducting 7T fMRI experiments in 
Vienna, data analysis

* Participation in scientific conferences and workshops

* Preparing scientific manuscripts and publications

* Contribution to supervising Bachelor and Master's theses

* Writing and submitting a doctoral dissertation at the end of the project



Your profile

* Master's degree or diploma in neuroscience, physics, biomedical engineering, 
computer science or similar fields

* Interest in the topic of the project and in vision/neuroscience research in 
general

* Sound knowledge in conducting (f)MRI experiments and analyzing (f)MRI data, 
preferably at ultrahigh magnetic field

* Excellent programming skills (MATLAB, Python, Linux shell, etc.)

* Excellent English skills

* Excellent organizational, communication and social skills, independence, 
reliability

* Preferably sound knowledge of the visual system

More information is available at 
https://secure-web.cisco.com/1QSEqOWvfyj3Fn-k_qchrTdPC3oPy2SGg1xDUvzx9ueGD8iYUaysM8qcH6lL3PA9lsnZdn59-Kx0Gc4fyvzEbKw26JDyWUGsCs-7rVAQzalNo0Gpa07i5xHiO6O_OD6JTEljxlB-8V_3MoO4d-b71WjOnHdyTaX6kYQeldJpfH94OEI2oQ8ZB1P6i41-h8HmpBQvpgrwDfjpwpBIIIweRYkMuK9psOB4K6OXVhzrJUzsgap5EjxOhPocYcQEmTFB3Ou983YOsSA7OFK9EfCbtjnkm5hsD63kS5W56MYdr9KWM5xqyWYXu1ltBZgXuSEF-dv4fmpwmAiYdmdvevMjgnQ/https%3A%2F%2Fneurovision.uni-graz.at%2Fen%2F
 , 
http://secure-web.cisco.com/13ejGmNm191wKTEtay0FeS3AMK97XGb6RNkQtfnvjwL2i2ZGRKublIkm46qq1-2noECEyVODgomzTmfdUB847dqIYKCIFA4Eo6RJhDCbLEyR8Juf06d6YL34nRd0MMooKy6wnxHaD_kTEh-Z9toj0CbX0a4RzWduYSZMD_kXK3VGUGoSSWnzYLZ-_gRZGDZZf_1MinBCVSCPMWNBDAwKXCe9teYHLghy3VwmHSqtclBnSC0qqR7KkQO_d0L8FTLCTq_rH4IuEqqdeyC_dRUdAAcxJiD0NdtcE0hTq1FPrXPIAI-IlJLEl9a_OzQTFU9HU1ptbfz7VossbBLPdeOO49w/http%3A%2F%2Fwww.fmri.at%2F
 and

[Freesurfer] Probability density function

[Jingjing Liu]

External Email - Use Caution

Dear Freesurfer team,

I am looking for the answer that where I can find the document of
Probability density function in voxels of each brain volume after
preprocessing. Because I need these indicators.

Thank you so much in advance for your reply!

Sincerely,

Jingjing Liu
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[Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar

[Carina Obermüller]

External Email - Use Caution

Dear Freesurfer team,

I am looking for a group stats command like the asegstats2table and 
aparcstats2table command for hipposubfields, brainstem and amygdalar, but I 
couldn’t find it in the archives. I remember it was mentioned in the recent 
Freesurfer course, but I can’t find it anymore. Could you help me out?
Also more generally, is there an overview page of all the possible group stats 
commands?

Thank you so much in advance for your reply!

Sincerely,

Carina


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[Freesurfer] how to resolve recon-all stopping at fill step

[Dong, Yilei]

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Dear FreeSurfer developers,

Apologies for emailing once again about how to resolve the recon-all stopping 
exactly at the fill step. I understand this may have to do with specific issues 
on UCSD's computer cluster, but if UCSD's cluster is not having the most 
up-to-date version of the FreeSurfer module, would it make a difference if I 
asked UCSD's supercomputer team to update the module version, so that the 
entire processing stream may be able to run all the way for 1 subject? Would it 
also make a difference if I increased the number of cores for 1 subject from 1 
to 2?

Sincerely,
Yilei
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[Freesurfer] Request to Edit Page (if possible)

[Emily Popa]

External Email - Use Caution

Hello,

I hope all is great. I ran into many issues using the -make flag with V 7.1 
(based on instructions found in 
https://secure-web.cisco.com/1-msyefLYicmgJRp4aaxIyvNgBvyxq1mdLLjw-c5oMGhWwhDIvsne4UVPuV8gJO1wRpU4IDqTHTP5ZSQSRSExq-uamYUsAELPzHCqbEvvXT3r6-emNpnSbqyEESd_8S-V5hdCs3JPxzJHjpK_0IWPJUw04Ix_ebgsE_nWusAYbTTV2kGzSqPgUyXnaccdtU8XTx1Mdj6hMpu6qV5RT9aeqX-0fwwskjqVfwyw2_YqbDURLomROl1CoWKQjr8JG9QPycqzb4OtZi62S7e9CBhrba_3bY_ecCztqxZMpnQd4xc9bQR2xGBg58Xf8BE8vazh5TabupP6qfnnCq_U-5zl_A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTroubleshootingData)
 and discovered after investigating erratic behavior/crashes across a bunch of 
re-processed cases that I had made edits to, that the functionality is no 
longer supported. I think it might be really helpful to others if at all 
possible to indicate this on the wiki where it is mentioned as it took some 
time to find the relevant post in the archives.

Thanks!

Best,

Emily S. Popa, M.S.
Programmer Analyst I, Neuroimaging
Pacific Brain Health Center | Pacific Neuroscience Institute Foundation | 
Providence Saint John’s Health Center
1301 20th St. #250 Santa Monica, CA. 90404
(408) 750-7971 (M)
[cid3519*image001.jpg@01D7EC78.96AA1AC0]
 [cid3519*image002.jpg@01D7EC78.96AA1AC0] 

  [cid3519*image003.jpg@01D7EC78.96AA1AC0] 

  [cid3519*image004.jpg@01D7EC78.96AA1AC0] 

  [cid3519*image005.jpg@01D7EC78.96AA1AC0] 


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[Freesurfer] Freesurfer on a high-performance cluster (HPC) - MATLAB runtime

[Camilo Castelblanco Riveros]

External Email - Use Caution

Hi all,

I hope your weekend is going great!

*Context*: I am trying to run the amygdala/hippocampus segmentation in an
hpc.
*Issue*: The cluster that I use doesn't have the libmwlaunchermain.so file
from MATLAB's 2019b runtime under
(/optnfs/freesurfer/7.4.1/MCRv97/bin/glnxa64).
Because I don't have permission privileges and standard bin/paths don't
apply in the hpc, I can't do something like fs_install_mcr.
*Question*: Does someone have the libmwlaunchermain.so file, or is there a
way to run the amygdala/hippocampus module without it? Any experience
with the hpc is helpful!

With gratitude,
Camilo

*Camilo Castelblanco Riveros (He/His)*
Integrative Neuroscience at Dartmouth (IND) Ph.D. Student
Robertson Lab 

 & Bujarski Lab

Diversity Student Advisory Board Member
e: ccastelblanco...@dartmouth.edu


[image: Integrative Neuroscience at Dartmouth (IND) (@DartmouthNeuro) /
Twitter]
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[Freesurfer] Unequal size groups

[stdp82]

 
 External Email - Use Caution
  Hi 
  I’m using fs-fast to map the connectivity differences between 3 groups. My problem is unequally sized groups. In the sense that the first group consists of 40 subjects, the second of 190, and the third of 18. What solutions does FreeSurfer offer to handle this type of problem which affects the assumption of equal variances in tests like ANOVA? 
  Thanks 
    
  Stefano
 

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[Freesurfer] mri_watershed Error: read failed

[Schroder, Kirsten]

External Email - Use Caution

Dear Freesurfer developers,

I am currently conducting a research project in which I am running 7T MP2RAGE 
images in Freesurfer version 6.0.1 but have a run into an issue.

For 3 images I receive a watershed error stating “mri_watershed error: GLOBAL 
region of the brain empty!” which I tried to fix using the -skullstrip 
-no-wsgcaatlas flag but get different results: 1 image was successful but for 2 
images I get mri_watershed Error: read failed (see attachment). It appears that 
the last file created is the  001.mgz file hence there is no T1.mgz file 
created and Freesurfer therefore gives this error. I wanted to know if there is 
way to fix this as I have not been able to find a successful solution from the 
archive. I have also run the same dataset in Freesurfer version 7.2.0 and 
receive the same error for some scans.

Any help would be appreciated.

Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
uname -a: Linux pc8-009.ion.ucl.ac.uk 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Mar 
21 12:19:18 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux

Thank you,
Kirsten

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[Freesurfer] Valid options.txt file for mris_pmake (and maybe .dsh.yml too)

[Garikoitz Lerma-Usabiaga]

External Email - Use Caution

Hi list!
I was reading the documentation on mris_pmake (by the way, it is outdated,
the documentation still asks for --surface00, at least in 7.3.2), and I
would like to have a valid options.txt file to make it work with dsh (a
valid example .dsh*.yml would be greatly appreciated too.

I want to speed up a simple vertex to vertex calculation, as Bruce said in
an old thread, I am able to run it line by line but there is a lot of
overhead reading the surfaces, so it would be great to just do the
calculations.

Thanks!!
Gari
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Re: [Freesurfer] Issue related to converting .nii.gz file to .mgz using FreeSurfer's mri_convert

[Huang, Yujing]

I'm trying to understand the issues related to mri_convert.

It looks like you did the following:
1. mri_convert aparc.DKTatlas+aseg.deep.mgz aparc.DKTatlas+aseg.deep.nii.gz
2. saved the manually edited as aparc.DKTatlas+aseg.deep.edited.nii.gz
3. mri_convert aparc.DKTatlas+aseg.deep.edited.nii.gz 
aparc.DKTatlas+aseg.deep.edited.mgz
3. MRIcron complained about the first number is not 1 when you tried to open 
aparc.DKTatlas+aseg.deep.edited.mgz (There is no error when you open 
aparc.DKTatlas+aseg.deep.mgz)

Which version of Freesurfer are you using? We changed the first number to 
encode the mgz_intent_code. In dev version of Freesurfer, the first number is 
not always 1 in .mgz. It is '((mgz_intent_code & 0xff ) << 8) | 1' depending on 
mgz_intent_code. In your case, it should be mgz_intent_code=0 and first 
number=1.

mri_info reports intent if you are using dev version.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Tsigaras, Thanos
Sent: Wednesday, May 15, 2024 4:38 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Issue related to converting .nii.gz file to .mgz using 
FreeSurfer's mri_convert


External Email - Use Caution
Hello FreeSurfer Developers,

I am using FastSurfer for this processing, but the issue is related to 
FreeSurfer's mri_convert function. I wanted to perform some manual segmentation 
edits on the "aparc.DKTatlas+aseg.deep.mgz" output file of FastSurfer. Since 
ITK-SNAP can't open .mgz files, I used the mri_convert function to convert the 
.mgz file to .nii.gz. I performed the edits and tried to rerun FastSurfer using 
the manually edited .nii.gz file. I got the error:

"ERROR: Specified segmentation output and conformed image output do not have 
same file type.
You passed --asegdkt_segfile directory/to/aparc.DKTatlas+aseg.deep.nii.gz and 
--conformed_name directory/to/orig.mgz.
Make sure these have the same file-format and adjust the names passed to the 
flags accordingly!"

So I used mri_convert once again to convert the .nii.gz file back to .mgz. When 
tried to rerun FastSurfer, I got the error:

"You passed --surf_only or --no_asegdkt, but the whole-brain segmentation 
(directory/to/aparc.DKTatlas+aseg.deep.edited.mgz) could not be found."

I also tried opening the .mgz edited file using MRIcron, but I get an error 
there as well: "Error: first value in a MGH header should be 1 (got 1) and data 
type should be in the range 1..4. (got 10)", which is not the case when I open 
the original .mgz file. The way I am using the mri_convert function is simply 
"mri_convert aparc.DKTatlas+aseg.deep.edited.nii.gz 
aparc.DKTatlas+aseg.deep.edited.mgz".

I've searched the list and no similar errors have been reported. Please let me 
know if you need more details to help me troubleshoot this issue. For your time 
and help I would like to thank you in advance!
Best regards
Thanos Tsigaras




Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens


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Re: [Freesurfer] error using mri_em_register

[Huang, Yujing]

There is an error in your first 'recon-all -autorecon1 -noskullstrip' attempt:
"
\n
ERROR! FOV=302.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
\n
"

You can't run recon-all '-autorecon2 -autorecon3' until you have successfully 
run autorecon1.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Michal Zamberg-Elad
Sent: Wednesday, May 15, 2024 7:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] error using mri_em_register


External Email - Use Caution
It does not create the nu.mgz file.

Error logs are attached.
The result is that when running recon all it cannot find the LH and RH files 
and then collapses.


Darwin Kernel Version 21.3.0
iMac-Pro 21.3.0
Root: xnu-8019.80.24~20/RELEASE_X86_64 x86_64

Thank you,
Michal
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[Freesurfer] error using mri_em_register

[Michal Zamberg-Elad]

External Email - Use Caution

It does not create the nu.mgz file.

Error logs are attached.
The result is that when running recon all it cannot find the LH and RH files 
and then collapses.


Darwin Kernel Version 21.3.0
iMac-Pro 21.3.0
Root: xnu-8019.80.24~20/RELEASE_X86_64 x86_64

Thank you,
Michal


recon-all.log
Description: recon-all.log
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[Freesurfer] Issue related to converting .nii.gz file to .mgz using FreeSurfer's mri_convert

[Tsigaras, Thanos]

External Email - Use Caution

Hello FreeSurfer Developers,

I am using FastSurfer for this processing, but the issue is related to 
FreeSurfer's mri_convert function. I wanted to perform some manual segmentation 
edits on the "aparc.DKTatlas+aseg.deep.mgz" output file of FastSurfer. Since 
ITK-SNAP can't open .mgz files, I used the mri_convert function to convert the 
.mgz file to .nii.gz. I performed the edits and tried to rerun FastSurfer using 
the manually edited .nii.gz file. I got the error:

"ERROR: Specified segmentation output and conformed image output do not have 
same file type.
You passed --asegdkt_segfile directory/to/aparc.DKTatlas+aseg.deep.nii.gz and 
--conformed_name directory/to/orig.mgz.
Make sure these have the same file-format and adjust the names passed to the 
flags accordingly!"

So I used mri_convert once again to convert the .nii.gz file back to .mgz. When 
tried to rerun FastSurfer, I got the error:

"You passed --surf_only or --no_asegdkt, but the whole-brain segmentation 
(directory/to/aparc.DKTatlas+aseg.deep.edited.mgz) could not be found."

I also tried opening the .mgz edited file using MRIcron, but I get an error 
there as well: "Error: first value in a MGH header should be 1 (got 1) and data 
type should be in the range 1..4. (got 10)", which is not the case when I open 
the original .mgz file. The way I am using the mri_convert function is simply 
"mri_convert aparc.DKTatlas+aseg.deep.edited.nii.gz 
aparc.DKTatlas+aseg.deep.edited.mgz".

I've searched the list and no similar errors have been reported. Please let me 
know if you need more details to help me troubleshoot this issue. For your time 
and help I would like to thank you in advance!

Best regards
Thanos Tsigaras




Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens


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Re: [Freesurfer] Hippocampus subfield LUT

[Douglas N. Greve]

Look in $FREESURFER/FreeSurferLUT.txt
This has those indices (and a lot more). If you want just the hippo SF 
indices, you can run something like

mri_segstats --seg hipposf.mgz --ctab-default --sum sum.dat
The indices will be in sum.dat

On 5/14/2024 11:04 AM, karl landheer wrote:


External Email - Use Caution

Hello, I am looking for the LUT which converts the indices in images 
like lh.hippoAmygLabels-T.v22.mgz to region name. Is this available 
anywhere? I can’t find it


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[Freesurfer] Hippocampus subfield LUT

[karl landheer]

External Email - Use Caution

Hello, I am looking for the LUT which converts the indices in images like
lh.hippoAmygLabels-T.v22.mgz to region name. Is this available anywhere? I
can’t find it
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Re: [Freesurfer] Retinotopy error computing contrast matrices

[Mesquita, Tiago]

External Email - Use Caution

Hello Freesurfer Experts,

I find a way to do the analysis solving the contrast matrices problem, but I am 
not sure about this solution, mostly because the results don't look correct to 
me.


So basically my solution was replicate my 3 runs, and the second time calling 
it Eccen after the first 3 being polar. This time the contrast matrix was 
created without any issue and the analyse was done.

So I would like to know if the problem is on my "solution". And if is there any 
way of doing eccen and polar separately.
How should I proceed with this analysis since i use bars that swipe the visual 
field, from 8 different directions, i think the can be considered as both eccen 
and polar because I'm covering different angles and different eccentricities.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Mesquita, Tiago 

Sent: 20 April 2024 14:29:19
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Retinotopy error computing contrast matrices


External Email - Use Caution

Hello FreeSurfer Developers,

I am trying to do a retinotopy analysis. My retinotopy has 8 bars, this bars 
swipe the visual field from the 8 possible directions (all multiple of 45 
degrees angle). One complete swipe takes 24 sec. I have 16 different positions 
per swipe. So I have tried using -retinotopy 24 (period of a complete swipe) or 
1.5 (period of each individual bar) in every case i always end up having the 
same error. For some reason Xcond = NaN (normalized). I tried eccen pos, eccen 
neg even polar neg and pos in my paradigm files and get always the same result.

Can someone help me? this is what i get:

Creating Design Matrix
 ... creation time =  0.006 sec
DoMCFit = 1
ntptot = 119, nX = 35, DOF = 84
Saving X matrix to ~/Project/Sess02/bold/rtopy.self.lh/pr001/Xtmp.mat
XCond = NaN (normalized)
Warning: Matrix is singular to working precision.
> In fast_selxavg3b (line 403)

Computing contrast matrices
Warning: Matrix is singular to working precision.
> In fast_selxavg3b (line 441)

Warning: Matrix is singular to working precision.
> In fast_selxavg3b (line 441)

OLS Beta Pass
  run 1t= 0.0
reading data ... 0.820008
Global Mean   146.10
Global In-Mask Mean = 146.104 (NaN)
Rescale Target = 100
RescaleFactor = 0.68
OLS Residual Pass
  run 1t= 0.0
reading data ... 0.776954
Saving rho1
Found 0 voxels with corrected AR1 > 0.90
Not Whitening
Warning: Matrix is singular to working precision.
> In fast_glmfit (line 54)
In fast_selxavg3b (line 999)

Found 7921 zero-valued voxels
Computing contrasts
Starting contrasts
eccen J=2 -
Warning: Matrix is singular to working precision.
> In fast_fratiow (line 86)
In fast_selxavg3b (line 1161)

Warning: Matrix is singular, close to singular or badly scaled. Results may be
inaccurate. RCOND = NaN.
> In fast_fratiow (line 86)
In fast_selxavg3b (line 1161)

Error using betainc
X must be in the interval [0,1].

Error in FTest (line 51)
p = betainc(z, dof2/2, dof1/2);

Error in fast_selxavg3b (line 1163)
pmat = FTest(dof1, dof2, Fmat);

If i look into the X.mat m betainc is filled witn NaN.

I have atteched my analysis info and X.mat.
Let me know if you need more informations about my analysis.

Best,

Tiago Mesquita
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[Freesurfer] Harmonization (Site/Scanner) for FreeSurfer Area Data

[Tejaswi D. Sudhakar]

External Email - Use Caution

Hi FreeSurfer experts,

I have harmonized across site and scanners on both thickness and area for a 
large cohort (500+ subjects).

We are seeing high covariance values when comparing the harmonized and 
non-harmonized area datasets and trying to understand what this means.

Can this be due to how area is calculated (the mean area of the adjacent 
triangles at a vertex)? Are all of the triangles the same size? Can you explain 
the calculation of area further in the context of how thickness and area are 
related?

Secondly, we haven’t seen much literature on harmonizing freesurfer area, 
though harmonization is well reported for thickness measures. Are you familiar 
with harmonization of area data?

Best,
Tejaswi
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[Freesurfer] Subcortical surfaces from volume features.

[Sam Maddox (CMP - Postgraduate Researcher)]

External Email - Use Caution

Dear Freesurfer Experts,

I am looking into generating subcortical surfaces from the subcortical volumes 
generated from recon-all. The reason for this is I am trying to create a vertex 
based Morphological Similarity Network generated from both cortical and 
subcortical regions. Ideally I would avoid Volume Based Statistics as, from 
what I can see, I am limited to just thickness features.

I have run recon-all for all of my participants, and ideally my set up for 
surface subcortical features would be done in freesurfer as well, although I am 
aware of other tools such as:
https://secure-web.cisco.com/1Naw6TVmVSgW4iHi_BvEcAItpkOmdAs3fMgTWn1abKwPfBB8rdZFU3uvsi4cPqx3S8bYQkyU527GS0tUWq5iTLIxi4h-neYTg3rRF4rm36g6ssGYvZTHYISx4xuiaDvdlgjLf00reXO6y4TRF6SOjlA2eclFajGQaaMj_WAPMydblg1WhHM3s49fAVOEYVpYz5DKxrM9HaIEbEhAUQfic1RPJW9C_WvN7qtqqxCGA2jBE5sAQ3gQdaiTi6ckB5Co2EaKd_919kOa34WJ6MXeQhIRrDU18ASd_y1u_AhvG__WBnPhcjqAzmFXgwtAXFQUeuXxMG33RICOWUxpS-QpFhg/https%3A%2F%2Fgithub.com%2FNIRALUser%2FSPHARM-PDM%3Ftab%3Dreadme-ov-file
https://secure-web.cisco.com/1u1Ru_EifdWYQsjg7F-GHFGBp-Vkvjk_3iHSqwgV0CTWKwS_FdITj126INHIN78MyDplkEgShMCUIlnKVgVAVeIL4pXXY0VzSExsLZPdSZzxjJkfX71D38cItZvMy0YpbKye--NNeT0bh3Tomd12EW1AAdNcOFsjDbbn_pa2ThIa_zYKV1RErGaiqR-uN33LV-JUKm-H6SrWEurQFUU9O-BLvIKrPcdGn_ZP7LhTJSQSzia576nMQtbhwz8k4uk9Tn3scHnFpNNJ-BdlV-VJmxSSTlz9c8vsy4woTK4TB-kkfz47AKxZg0RU8oilcgIikrfo_kO5HCoQwAMqTqxsJhA/https%3A%2F%2Fgithub.com%2Fthomas-vincent%2Fnipic%2Fwiki%2F%255BFreesurfer%255D-Get-surfaces-of-subcortical-structures
https://secure-web.cisco.com/1yhlZBs4CaRuE7OrwrGVtEsQL33d47WfL9Yu02tKHEzKqGis-VZ2QsUo3wc0I-F9Xl4CD42o42gUtGEvKCz8usWl7X-3fhwsXAu2DKmngoloe8OIoLcqBvxP7uX_nAUAOzJVhL1v1X1wGpSSCDx2i646Rrxd1R0iGBv28T3TEcEzQA7Mfpl98Tse0ab3SdW04eOZHbRzG0bqADUjE7WXLR3jQUj9GAT4IkULnuGhhv7CP9gF2IIOAaNcBqU8xsijZDxWuelDUPELsRrWlxOJ6HSBWWntUhP7GZF336sA8O4ErBZai7rjk2BwMvCxskkvPYYEduQ_YepFNicYE-rsWnA/https%3A%2F%2Fgithub.com%2Fkhanlab%2Fsurfmorph
https://secure-web.cisco.com/1SH8G6D-66tFkOVdkMhKlZU3DoZJWFrankZvFbDjhud520NPLJFMbPVEY3QEkx1Anjs_T-mOZ802DkO8IMAoKICsuHGbfGHzlCBpuLpBo3eG6xOMEBAvyPoDJp4Foco_c278n-AKuUSqWStoiyqybIWHuEDnEVXSCFHtEcCER3WFc7Y05QDcELHJxcVyfuqIM49409LcHzosBJuWF2rTNTteyik5rMYdclhak8oiyez2cmqdIO_JRAajAd0aadfNPhe0A7A41RkGowT8gzaCssM-DEIHPy8MjjNu8X8iL8dp0yAyktpa1nICSQP4S41QtHxJqzOkF7bZHOU6xFerjNA/https%3A%2F%2Fgsl.lab.asu.edu%2Fmtsms%2F
inaivu/aseg2srf at master * aestrivex/inaivu * 
GitHub

The above tools may be able to generate subcortical surfaces, but I would then 
need to convert them back to freesurfer formats to run mris_anatomical_stats, 
which I am lost with. If anyone has any advice for this, this would be great!

Within freesurfer, I am aware of tools such as mri_vol2surf, as well as other 
such as mris_sample_parc - Free Surfer Wiki 
(harvard.edu).
 I am a bit lost as to how to use these tools, as the documentation is limited, 
and threads are more looking at generating these surfaces for visualizations 
rather than anatomical statistics.

I am also wondering if there are any additional processing steps, perhaps 
normalization, that may be required before creating the MSN.

If anyone has tried this before or has any advice, I would love to hear. I am 
relatively new to this area, using freesurfer past recon-all, so any help is 
appreciated!

Many thanks,
Sam
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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

[Liliana Wu]

External Email - Use Caution

Thank you Douglas. That’s much clearer. I do however,  have a subject without a 
gender disclosure. Would I set up my class and contrasts as:

5 classes: PatentientsMale, PatientsFemale, HCMale, HCFemale, HCNa


then use contrast [0.5 0.5 -0.33 -0.33 -0.33 0 0 0 0 0 ...]?



Best,
Liliana

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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

[Douglas N. Greve]

The first one will test for a difference between group offset/intercept 
accounting for age, gender, episodes, and residuals. By setting a 
regressor contrast element to 0, one accounts for that variable because 
the variable appears in the model that is fit to the data (and so its 
effects already removed from other variables). One more thing: I would 
recommend incorporating gender in the class structure not as a 
continuous variable. So you would have 4 classes: PatentientsMale, 
PatientsFemale, HCMale, HCFemale then use contrast [0.5 0.5 -0.5 -0.5 0 
0 0 0 0 ...]


On 5/9/2024 3:26 PM, Liliana Wu wrote:


External Email - Use Caution

Hello!

I am having trouble with creating my contrast files. I did go over 
FsfdExamples (*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples 
). 
However, I am unsure how should I create my contrast files if I want 
do a 2 group comparison while controlling 4 covariates:


Class:

Patients, healthy control

variables are:

Age,gender,episodes,residuals,

Here is how I set up my contrast files:

1 -1 0 0 0 0 0 0 0 0  - Contrast1 (measure group differences)

1 -1 0.125 0.125 0.125 0.125 0.125 0.125 0.125 0.125 – Contrast 2 
(measure group differences while accounting for covariates)


For some reason I think I am setting up those contrast files wrong… 
Any help is appreciated.


Best,

Liliana


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[Freesurfer] mri_segment_hypothalamic_subunits 7.4.1 issue

[Antonio Di Renzo]

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Dear FreeSurfer developers,

I have just tested the Segmentation of hypothalamic subunits, but unfortunately 
it does not work.
I simply wrote:

mri_segment_hypothalamic_subunits --s subject_folder

or

mri_segment_hypothalamic_subunits --s subject_folder/T1.nii

or

mri_segment_hypothalamic_subunits --s recon_all_processed_folder

Every time the message is: Illegal instruction (core dumped).

Moreover when I asked the help option:

mri_segment_hypothalamic_subunits -h

I obtained again: Illegal instruction (core dumped).

I installed tensorflow as answered using:

fspython -m pip install tensorflow

 but these libraries are installed already because the messages are: 
Requirement already satisfied written on every row.

How can I use this function?

Thank you in advance,

Antonio



ps. I used the following softwares

Freesurfer version 7.4.1

Ubuntu 22.04.4 LTS

Oracle virtual box for Windows 10 pro
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[Freesurfer] Contrast files - 2 groups, 4 covariates

[Liliana Wu]

External Email - Use Caution

Hello!

I am having trouble with creating my contrast files. I did go over FsfdExamples 
(https://secure-web.cisco.com/1ezcK_pFVwJfmWpdVsJeZORU_8kaDi3SfZnw3BO98zpMkJch-p_v87YwJzoqtiefk_hIobUKYja2omqZRjod-i1GdU-HkzipUmBlo5LVsklOHdteQtjAi1L5l1J_T5iRzcE-h_C2xiFxUcjQxPmDrQFVFDP-mFdgiDx4hibkUidw4NEsFW1XHiR7roksIT1GrgvmbILffvuecnvDO6Z8oTqSldk1jddeE0vQYO5WHK19PUmdcg_uW0gtN1EgAhq3AxmE2NcKh2djkfca5f3nqamoDBZ84nG1kz_J43CQgPHPe_lX5eVqUfcsPGuqiMUbpt15_ZNoCDBTS88hFbjyFVA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples).
 However, I am unsure how should I create my contrast files if I want do a 2 
group comparison while controlling 4 covariates:

Class:
Patients, healthy control

variables are:
Age,gender,episodes,residuals,


Here is how I set up my contrast files:

1 -1 0 0 0 0 0 0 0 0  - Contrast1 (measure group differences)
1 -1 0.125 0.125 0.125 0.125 0.125 0.125 0.125 0.125 – Contrast 2 (measure 
group differences while accounting for covariates)



For some reason I think I am setting up those contrast files wrong… Any help is 
appreciated.

Best,
Liliana

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Re: [Freesurfer] MCR install for parcellation

[fsbuild]

External Email - Use Caution

Hello Antonio,
With the 7.4.1 release, you can install R2014b or R2019b matlab runtime 
environment into the freesurfer tree. Earlier freesurfer releases use 
R2014b. I would setup the freesurfer environment first, and then pass in 
the value of FREESURFER_HOME on the command line as listed below. Below, 
I have shown using R2019b with a linux install of Freesurfer 7.4.1 using bash 
shell.
- R.
- - - - -
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
 --- linux install path
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
... output deleted ... showing SUBJECTS_DIR and other environment 
variables
$ cd $FREESURFER_HOME/bin
$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
I believe this sets things up (for R2019b) so the libmwm* libraries are 
installed under $FREESURFER_HOME/MCRv97/bin/glnxa64. You can try adding 
that path (or any path the fs_install_mcr script output recommends) to the 
start of LD_LIBRARY_PATH. You should remove any other entries to a 
different MATLAB distribution other than the one you actually install.
On May 9, 2024, at 12:45, Antonio Di Renzo antoniomp...@hotmail.it 
wrote:External Email - Use 
CautionMessers FreeSurfer 
developers,I dowloaded MCR zip file for linux in /home/vboxuser/Downloads from 
MatLab website.I extracted files in new foldern named 
Matlab_Component_Runtime_R2014b in Downloads.I am trying to install Matlab 
Component Runtime, but the the following command:fs_install_mcr R2014b 
does not work.Where can I find the right step by step MCR installation 
guide?Thank 
you,Antonio___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] MCR install for parcellation

[Antonio Di Renzo]

External Email - Use Caution

Messers FreeSurfer developers,

I dowloaded MCR zip file for linux in /home/vboxuser/Downloads from MatLab 
website.
I extracted files in new foldern named Matlab_Component_Runtime_R2014b in 
Downloads.

I am trying to install Matlab Component Runtime, but the the following command:

 fs_install_mcr R2014b does not work.

Where can I find the right step by step MCR installation guide?

Thank you,

Antonio


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[Freesurfer] Postdoc Positions in Cognitive Neuroscience/ Neuroimaging Genomics

[X K]

External Email - Use Caution

Postdoc positions are available at Zhejiang University (Hangzhou, China).
The successful candidates are expected to work on multi-disciplinary
projects in cognitive neuroscience, neuroimaging and computational
modelling related to individual differences in language/spatial navigation,
relevant brain networks, aging and disorders.

The Cognomics Lab is led by Dr. Xiangzhen Kong, who has extensive
experience in cognitive neuroscience and the application of computational
modelling and neuroimaging genetics to investigate functional architecture
of the human brain and how it supports human-defining cognition. We conduct
large-scale studies using a variety of data sources including in-house
datasets (e.g., fMRI, SEEG), and open data from UK Biobank and ENIGMA.

We seek highly motivated candidates with a Ph.D. degree in cognitive
neuroscience, psychology, bioinformatics, or computer science with
biomedical applications, etc. The ideal candidates should be highly
motivated to publish first-author papers and present at conferences, and
are expected to have strong quantitative skills and experiences in
programming and machine learning.

Interested applicants should submit a CV, a letter briefing current
research interests, and contact information for two individuals who can
provide letters of recommendation to Dr. Xiangzhen Kong
(*xiangzhen.k...@zju.edu.cn
*).

Positions will remain open until filled.
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[Freesurfer] Incorporating hi-res T2w image in longitudinal pipeline

[Raikes, Adam C - (adamraikes)]

External Email - Use Caution

Good afternoon,

We are collecting hi-resolution T1w and T2w images (0.8mm3) in a pre-/post- 
design. I am using Freesurfer 7.4.1 to process the data and have been 
successful in ingressing the T2w images in the cross-sectional recon-all runs 
with -T2  and -T2pial.

Two questions:

  1.
When creating the base image, is there any value to using the T2s and, if so, 
is there a way to do that?
  2.
When running the -long step, I know that -T2pial is an option but do I need to 
pass -T2  with it? If I need the path, should it point to the original 
image or something from the cross/mri folder?

Thanks


Adam C. Raikes, PhD

Imaging Projects Manager

Center for Innovation in Brain Science

University of Arizona


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Re: [Freesurfer] outcome directions of longitudinal two stage model

[L]

External Email - Use Caution

Yes, I was wrong in considering tp1 - tp2 or tp2 - tp1. Actually, my
question is: If the changing rate or % in thickness of a region calculated
using long_mris_slopes is a positive number, does that mean it's an
increase in thickness from baseline (or tp1)?

Thank you,

Lihong

On Wed, May 8, 2024 at 9:35 AM Douglas N. Greve 
wrote:

> not sure what you mean and/or referring to. can  you elaborate?
>
> On 5/7/2024 4:03 PM, L wrote:
>
> External Email - Use Caution
>
> Dear exports,
>
> I am wondering whether the outcomes of the longitudinal two stage model is
> tp1 - tp2 or tp2 - tp1.
>
> Thank you,
>
> Lihong Wang
>
> --
> - Lihong
>
>
> ___
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>  .
>


-- 
- Lihong
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Re: [Freesurfer] surface and cortical thickness normalization

[Douglas N. Greve]

The reason I suggested scaling by eTIV is an analogy with a box of 
paper. The surface area of the paper in the box scales linearly with the 
volume in the box (twice the volume, twice the paper, twice the area). I 
vaguely remember doing a test of this, but, if I did, it has been a 
while. probably using eTIV^(2/3) works well too. I don't think it is so 
important that it be unitless (though maybe it is easier at review time).


On 5/3/2024 10:56 AM, Fischl, Bruce R.,PHD wrote:


Hi Yunus

I think typically you would normalize by eTIV^(2/3), which would 
result in a dimensionless scaling


Cheers

Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *yunus soleymani

*Sent:* Friday, May 3, 2024 3:31 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] surface and cortical thickness normalization

*External Email - Use Caution *

Hello,

I hope you are doing well. Yesterday, I had some questions regarding 
normalization in Freesurfer. Thanks to Dr. Douglas N. Greve, I 
received answers for all of them. However, I still have one more 
question.


When I normalize brain surfaces to eTIV, they appear to be in two 
different units (mm2 and mm3). Will this be a problem? Additionally, I 
would like to know your thoughts on normalizing cortical thicknesses. 
Do you think they should be normalized to eTIV, or would it be better 
to normalize them to the mean cortical thickness of each subject?


I would greatly appreciate your response.

Thank you,
Yunus


*Yunus Soleymani*
**
*Ph.D. Candidate of Neuroimaging *
*/Tehran University of Medical Sciences/*
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+98 914 526 9298


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Re: [Freesurfer] Difference between 2 ways to set up fsgd file and contrasts

[Douglas N. Greve]

They are not identical, for  sure. In general, I discourage people from 
modeling categorical variables (eg, Group1/2 below) as continuous 
variables because you make assumptions that might not be reasonable (eg, 
females will have twice the thickness as males). I would use the first 
method.


On 5/2/2024 8:20 PM, Lydia Chung wrote:


External Email - Use Caution

Hi FS support team,

I am going to be using mri_glmfit to test 1) main effects (which 
regions show differences in cortical thickness between group 1 and 
group 2) and 2) interaction effects (does the relationship between IV 
and DV depend on moderator). Depending on the model, the IV is 
sometimes a binary categorical variable and sometimes a continuous 
variable. The moderator is always continuous. So, interaction effects 
are either continuous x continuous OR categorical x continuous.


One thing I'm trying to understand is whether the two examples below 
are basically two different approaches that answer the SAME question: 
Do people in Group 1 differ from Group 2 on cortical thickness? 
Version 1 is the one provided by FS and Version 2 is an analog of 
another setup I have been provided by colleagues. Are these models 
answering the same or different questions? The freesurfer link below 
also shows an example of how to do an interaction (Group x Age) using 
Version 1 setup; for Version 2 setup of an interaction, I know I would 
multiply the IV and Moderator before this step so that I would have an 
additional "interaction variable" column to add as one of the 
'Variables' listed in the fsgd code.  So, I'm also curious if the two 
different methods of testing an interaction (in addition to the first 
question about the main effect) will get you the identical answer OR 
if there is something conceptually different? Do the nuances of this 
setup have to do with the difference between using DODS or DOSS?


_
_
_Main effect of Group on cortical thickness Version 1 (copied from FS 
example. link here 
)_

GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
Variables Age Weight
Input subject1 Group1 30 100
Input subject2 Group2 40 120

Contrasts: 1 -1 0 0 0 0 (to test main effect of group; this feels like 
an anova approach?)


_Main effect of Group on cortical thickness Version 2_
GroupDescriptorFile 1
Title OSGM
Class Subjects
Variables Group Age Weight
Input subject1 Subjects 0.5 30 100
Input subject2 Subjects -.5 40 120

contrasts: 0 1 0 0 (to test main effect of group; this feels like a 
linear regression approach?)


Thank you in advance for your help!

Lydia
--


Lydia Wu-Chung, M.A.
Doctoral candidate
BMED Lab
Department of Psychological Sciences
Rice University
6500 Main St - MS201
Houston, TX 77030
Lab Phone: 713-348-8126
Email: lydia...@rice.edu 

_
_

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Re: [Freesurfer] outcome directions of longitudinal two stage model

[Douglas N. Greve]

not sure what you mean and/or referring to. can  you elaborate?

On 5/7/2024 4:03 PM, L wrote:


External Email - Use Caution


Dear exports,

I am wondering whether the outcomes of the longitudinal two stage 
model is tp1 - tp2 or tp2 - tp1.


Thank you,

Lihong Wang

--
- Lihong


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

[Douglas N. Greve]

It should just run the fill step. However, I've been slowly 
reprogramming recon-all to just see what needs to be run and rerun it, 
so you might get more than just the fill.


On 5/3/2024 4:38 PM, Dong, Yilei wrote:


External Email - Use Caution

Hi Freesurfer Developers,

Just to reply to this thread again, if I want to see if recon-all will 
just run the -fill step, do I submit it on the files that have already 
been run? In addition, does this error count as Freesurfer running out 
of RAM or it's more of a cluster issue I have to talk with the staff 
that manage it?


Sincerely,
Yilei

*From:* Dong, Yilei 
*Sent:* Tuesday, April 23, 2024 3:34 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] recon-all process still not finishing 
properly

Hi Freesurfer support,

I have several questions regarding recon-all -fill and -debug.

If we run recon-all -fill, what is the command set-up for that? From 
the ReconAllDevTable here, *MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable 
, 
do we structure the recon-all command to be: recon-all -autorecon2 
-fill -subjid ? I attempted to run recon-all -fill with -debug 
with the structure as follows: recon-all -s $subject -i $1 -fill 
-debug and I was wondering if this was the wrong format. I have also 
attached our recon-all-slurm-apr19.sb cluster submission file for 
reference.


Does recon-all -fill only run the fill step, while ignoring the 
previous steps before that or does recon-all run through all the 
initial steps including the -fill step ideally?


Regarding recon-all -debug, does the stdout file have the huge amounts 
of text specifying what each line is doing? I have included .out and 
.err files from the same recon-all -fill with -debug command for 
reference.


Sincerely,
Yilei

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


*Sent:* Thursday, April 18, 2024 2:57 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] recon-all process still not finishing 
properly
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:


External Email - Use Caution

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

Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

[Dan Levitas]

External Email - Use Caution

Hi Kersten,

If that's alright with you then that would be great. I completely accept if
my threshold is accurate and leaves no significant findings, I just can't
find a comparable threshold on this forum or elsewhere with such an
elevated threshold value.

I can touch base next week to see what you need from me.

Thanks again,

Dan

On Tue, May 7, 2024 at 3:09 PM Diers, Kersten /DZNE 
wrote:

> Hi Dan,
>
> I can see no obvious issues at the moment, but am happy to take a closer
> look when I am back in office next week.
>
> The fslmer tool ist just an R Implementation of the Matlab scripts, so I
> don't see any need to use them in your case.
>
> Best,
>
> Kersten
>
> Gesendet von Outlook für Android 
> 
>
> --
> *Von:* Dan Levitas 
> *Gesendet:* Dienstag, Mai 7, 2024 7:11:58 PM
> *An:* djlevitas...@gmail.com 
> *Cc:* kersten.di...@dzne.de ;
> mreu...@mgh.harvard.edu ;
> freesurfer@nmr.mgh.harvard.edu 
> *Betreff:* Re: [Freesurfer] Lingering questions for Longitudinal
> spatiotemporal LME analysis
>
> CAUTION: This email originated from outside of DZNE. Do not click links
> or open attachments unless you recognize the sender and know the content is
> safe.
> ACHTUNG: Dies ist eine externe E-Mail, bitte seien Sie vorsichtig beim
> Anklicken von Links oder Öffnen von Anhängen
>
> Hi Kersten & Martin,
>
> I just wanted to ping this thread again, as I'm still unsure about my pcor
> value (4.4) that I'm getting. I've seen other posts where the threshold
> (thmin) value specified in functions such as *mri_surfcluster* are around
> 2 (corresponding to a p-value of 0.01) when threshold *sig.mgh file(s).
> Given that I'm interested in both right and left hemispheres, I'm surprised
> that my single threshold value to account for both hemispheres is so high
> relative to others posts I've come across in the forum. I seem to have
> followed the LME approach correctly (
> https://secure-web.cisco.com/1SQ58WEznZe-ibw3QO19omrHSeej1iX-z28jkMlUtsQ61ntFqO78Z5WsmZPKSefBlApX7ijnNUsVb2PiYTMcLSHgq5Hf73E1qeczBabjq91RDS_J8NHpKFXZcedng6CSw5Dslno59UqFqwqKe0MlynvG0fLgW9CmBvYVyJOMfjqOkUnj-mZQrmtPHn6QGW9EgT6h77RTNNDYi3JzDqC5D-8yvOGOGy_rD2YAqFsyCnmAEdNhiGyU9zP2ii1jchj6eNZzKhgEp6ddY9VNl7yxVdP8JVkPxnFrj87WLBBrvjJrY7zXnrji5tdpZjvFiwVJQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels)
>  but
> I'm unsure if I've done something that has resulted in an elevated pcor
> value.
>
> Martin had recommended the *fslmer* tool (
> https://secure-web.cisco.com/1k8MMiLU-B44BypnewP6obBaoWvRatpcAdkGjbKYO0VGEedf5voupfVkhQXTbs8FThmGd4k5YzTCjcadNDPYbJvVhxCb-iyEmORVnucke7TNUZJKLtAvZmqGquU-VGxTC1N3bTuFZox3yd6f3tKd1Rk37nNQ7paxYwYXE-abGIb4qGHlxAecu3On7dDBTVotVlBChle8YVCs1qrJSKBkOe9Szvup6SomFsZzegV5ZSHpBJnVpNgH6vZYwY_Si4OOvW2M1ZhCLPfN_3zy75ccIM-x39bDlZKH9EWWAEIqYmvpVs6mp4CuDMHgJdI5t19o9rFDy-P4Gw8E3bHc8IJLjSA/https%3A%2F%2Fgithub.com%2Fdeep-mi%2Ffslmer),
>  I'd be happy to use that instead if
> it's more current and the preferred tool for this kind of analysis.
>
> Thanks again,
>
> Dan
>
>
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[Freesurfer] outcome directions of longitudinal two stage model

[L]

External Email - Use Caution

Dear exports,

I am wondering whether the outcomes of the longitudinal two stage model is
tp1 - tp2 or tp2 - tp1.

Thank you,

Lihong Wang

-- 
- Lihong
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Re: [Freesurfer] ERROR: cannot find AntsN4BiasFieldCorrectionFs in path

[Huang, Yujing]

Here is the wiki help page to setup and config your FreeSurfer:

https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Christine Farrugia
Sent: Tuesday, May 7, 2024 1:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ERROR: cannot find AntsN4BiasFieldCorrectionFs in path


External Email - Use Caution
Hi,

I have installed FreeSurfer (freesurfer-linux-centos7_x86_64-7.4.1) into my 
research group's directory on the University cluster, using the tar archive. I 
source it with

GROUPDIR=
export FREESURFER_HOME=$GROUPDIR/software/freesurfer
. $FREESURFER_HOME/SetUpFreeSurfer.sh
export PATH=$FREESURFER_HOME/bin:${PATH}

and am trying to run recon-all like so:
recon-all -s  -i  -T2  -T2pial 
-autorecon-all

However, FreeSurfer keeps giving the error:
ERROR: cannot find AntsN4BiasFieldCorrectionFs in path

when AntsN4BiasFieldCorrectionFs is definitely in freesurfer/bin

Any insight into the matter would be greatly appreciated 

Regards,
Christine
The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh 
Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
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 .
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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

[Dan Levitas]

External Email - Use Caution

Hi Kersten & Martin,

I just wanted to ping this thread again, as I'm still unsure about my pcor 
value (4.4) that I'm getting. I've seen other posts where the threshold (thmin) 
value specified in functions such as mri_surfcluster are around 2 
(corresponding to a p-value of 0.01) when threshold *sig.mgh file(s). Given 
that I'm interested in both right and left hemispheres, I'm surprised that my 
single threshold value to account for both hemispheres is so high relative to 
others posts I've come across in the forum. I seem to have followed the LME 
approach correctly 
(https://secure-web.cisco.com/1P1DqCgATuRJ8Gb_Cv23uM_tkjhG63bDl2SmrFrqCZVQtvVbHQS8mBMjen-kyKVz-FHDOZkAsJGG1DVRGpaFKTeDjg018Mg7Us0gCiJuSt9wg8P0AVc4qSxJSnKSMX6mnBthVdKpPGHWNhlm54QJHIPPywgoXMjN_75H-aApJpFyRuFMwk-5fsy7NNGvq6Bt7D_aTkcmqOCRPc0Qhtao7PTC1Wa647zPjfC5WMvogY318nyXI-NDKST7SgFOO8lrWe4OOR1B8D6vY3hvbW60vWm_asRrwMN5eaQ4dmhsyeCVMQB6pM_C2cmoEkNkH90ic-sFaG5UcQPlLLrLXyH_9Ww/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels
 
)
 but I'm unsure if I've done something that has resulted in an elevated pcor 
value. 

Martin had recommended the fslmer tool 
(https://secure-web.cisco.com/1f2ZYTXcSbFY4HqsjtbVZ5WFtQdhPr_P5UgrBHbi4cv6tXzH9AkMoC49SJidvN8KOesUL__-7wJaz-w-YBO9-JLSgN-s66cA_ATb3O9uESFLHsGDAHIbpXGV0NQzjMbccK9zFntec0iXjIoPF7pS67PhEIMRzIXxcsGD0vhclVwy1UQRFHr1IeNdNkvX57ShVW4OFh4LlDgaf5pdSCwvZw02TguHSSdl2cDidGQzWF_BZATX7IJkhDlP6JYZOLRlxCZmGhc6MdZhqsffzL7jzj64OW0O_fkZFOIFXlEzv780lDOHQINb51LAEeV7Ub0GsuwuuqNOHogzoUM9c0iLSIw/https%3A%2F%2Fgithub.com%2Fdeep-mi%2Ffslmer
 
),
 I'd be happy to use that instead if it's more current and the preferred tool 
for this kind of analysis. 

Thanks again,

Dan___
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[Freesurfer] ERROR: cannot find AntsN4BiasFieldCorrectionFs in path

[Christine Farrugia]

External Email - Use Caution

Hi,

I have installed FreeSurfer (freesurfer-linux-centos7_x86_64-7.4.1) into my 
research group's directory on the University cluster, using the tar archive. I 
source it with

GROUPDIR=
export FREESURFER_HOME=$GROUPDIR/software/freesurfer
. $FREESURFER_HOME/SetUpFreeSurfer.sh
export PATH=$FREESURFER_HOME/bin:${PATH}

and am trying to run recon-all like so:
recon-all -s  -i  -T2  -T2pial 
-autorecon-all

However, FreeSurfer keeps giving the error:
ERROR: cannot find AntsN4BiasFieldCorrectionFs in path

when AntsN4BiasFieldCorrectionFs is definitely in freesurfer/bin

Any insight into the matter would be greatly appreciated 

Regards,
Christine
The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh 
Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
___
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Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
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Re: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in CTAB colortable_vpnl.txt

[LYU, TIANXIANG]

External Email - Use Caution

Dear Yujing

Thanks a lot !!!
It is my fault. When I build this freesurfer, there are some files do not
correctly located in the install directory. Then I just copy them from a
x86 cluster. However, because I'm using the latest version from git, there
are some difference between this two version.
The warnings you mentioned are the small bugs of the system, please ignore.
Here's the context of
/vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt. I
think it is wrong.

login3$ cat
/vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt
# This is an LUT for the Juelich ytoarchitectonic atlas surface labels
created by Dr. Kalanit
# Grill-Spector's Lab at the Stanford Vision and Perception Neuroscience Lab
# See 
http://secure-web.cisco.com/1x8F5IrihAeNnPlynD7_olcHXVSCyGjMFfs6xdqCDrtm6LdZrUb-RBs19D1KW8JxL66wkzA8cbpOneaIxh34PoxhQvBCMajZI7gFtSUkFW2Y2Q463gII7an90KKIk7gPLiS7kY4JQ4qASc9Zu8y68SSThAco3yFPPEgVhbT5Lz_6T77zHxdonNU3zRPEzTl1VohnKIVaOOEhPseKIKFsFDUXhh17C-wL8sFdz6PKnury1csjjw6k5NAmvRitgCeJvMzkOGQhKjceepRCeXXGo8UfkEDkD2h9TZJQYN0BrOKReTiawTpCjFxIFARFOUDeb/http%3A%2F%2Fvpnl.stanford.edu%2FvcAtlas
# Ref:  Rosenke, M., Weiner, K. S., Barnett, M., Zilles, K., Goebel,
# R., Grill-Spector, K. (2017). A cross-validated cytoarchitectonic
# atlas of the human ventral visual stream. NeuroImage,
# 
http://secure-web.cisco.com/1p99Xaij8ZyvGzIoi_dK2BOanzxbIArwmyfHduwxdPLnMCKXwtiL37Vsvl44pqaz_1cBQrUxAexgh1T14U-YBgxZEUYHwYF4_dfSCetWSGUXeuMovhwnRFS2mx_PdBLhhyxEc1rH5wD744qpOAeUWhOhj8yo-wf_hNEgaqYUAh5jaunVxJQoK7BtQ4wA321IScwMbJqvHqKp--c3_l0j2_CwoBKvtfYG0KVR49qaFXxDmXnvCSMuGMjmBCqy2m65gOCYcvzAKfNC93xYgv16bItKTcOxKgcNOxaYBo1MxtgHeTC5xfdIYtqF5btFkduGP/http%3A%2F%2Fdx.doi.org%2F10.1016%2Fj.neuroimage.2017.02.040
 1  FG1 57   25520 0
 2  FG2255 0   255 0
 3  FG3  0 0   255 0
 4  FG4109 726 0
 5  hOc1 0   100 0 0
 6  hOc2   255 0 0 0
 7  hOc3v0   255   255 0
 8  hOc4v  255   255 0 0

In
https://secure-web.cisco.com/1rL_wmTmlepQKLEY0nBYoGUCBDcZbJgmQoAKwfu58LxxgoQEMTqigXChGfTFTfKtPl87SSo9xQyiZhgEJIjXr4XuYvSoVjQt1n9NyiPgHr0SHbydZklvFzuUzSJR7VBX5dg7TzqyEvjzYO2Htp4J1kgl09uZFaL2S1ExBlvPIO5zRai-GMb3fCQNBzUixWjtjKcxmdukEjNeqlRFaYiWar7hqdD8RsHuEkx5mXecqto_rj7cWwB6jLoDFPgKR3mzIwdArepX-4CK0XeGowTQPu0Iob2jY-St_1UDKgxyIHYvk9vm0uh9jZQzySFhqBbEg/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fdistribution%2Faverage%2Fcolortable_vpnl.txt,
it should be:

# This is an LUT for the Juelich ytoarchitectonic atlas surface labels
created by Dr. Kalanit
# Grill-Spector's Lab at the Stanford Vision and Perception Neuroscience Lab
# See 
http://secure-web.cisco.com/1x8F5IrihAeNnPlynD7_olcHXVSCyGjMFfs6xdqCDrtm6LdZrUb-RBs19D1KW8JxL66wkzA8cbpOneaIxh34PoxhQvBCMajZI7gFtSUkFW2Y2Q463gII7an90KKIk7gPLiS7kY4JQ4qASc9Zu8y68SSThAco3yFPPEgVhbT5Lz_6T77zHxdonNU3zRPEzTl1VohnKIVaOOEhPseKIKFsFDUXhh17C-wL8sFdz6PKnury1csjjw6k5NAmvRitgCeJvMzkOGQhKjceepRCeXXGo8UfkEDkD2h9TZJQYN0BrOKReTiawTpCjFxIFARFOUDeb/http%3A%2F%2Fvpnl.stanford.edu%2FvcAtlas
# Ref:  Rosenke, M., Weiner, K. S., Barnett, M., Zilles, K., Goebel,
# R., Grill-Spector, K. (2017). A cross-validated cytoarchitectonic
# atlas of the human ventral visual stream. NeuroImage,
# 
http://secure-web.cisco.com/1p99Xaij8ZyvGzIoi_dK2BOanzxbIArwmyfHduwxdPLnMCKXwtiL37Vsvl44pqaz_1cBQrUxAexgh1T14U-YBgxZEUYHwYF4_dfSCetWSGUXeuMovhwnRFS2mx_PdBLhhyxEc1rH5wD744qpOAeUWhOhj8yo-wf_hNEgaqYUAh5jaunVxJQoK7BtQ4wA321IScwMbJqvHqKp--c3_l0j2_CwoBKvtfYG0KVR49qaFXxDmXnvCSMuGMjmBCqy2m65gOCYcvzAKfNC93xYgv16bItKTcOxKgcNOxaYBo1MxtgHeTC5xfdIYtqF5btFkduGP/http%3A%2F%2Fdx.doi.org%2F10.1016%2Fj.neuroimage.2017.02.040
 1  FG1.mpm.vpnl 57   25520 0
 2  FG2.mpm.vpnl255 0   255 0
 3  FG3.mpm.vpnl  0 0   255 0
 4  FG4.mpm.vpnl109 726 0
 5  hOc1.mpm.vpnl 0   100 0 0
 6  hOc2.mpm.vpnl   255 0 0 0
 7  hOc3v.mpm.vpnl0   255   255 0
 8  hOc4v.mpm.vpnl  255   255 0 0

Sincerely,

Tianxiang Lyu
Graduate School of Medicine,
Juntendo University


Huang, Yujing  于2024年5月7日周二 21:57写道：

> Can you check if the colortables from your install directory agree with
> git repo?
>
> /vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt
>
> /vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt
>
>
>
>
>
> In your recon-all.log, there are a lot of warning messages like the
> following. I don’t know what that means.
>
> “
>
> [WARN] xos LPG 2002 - Failed to map HugeTLBfs for data/bss: /usr/bin/sed
>
> The e_type of elf header must be ET_EXEC when using libmpg. You can check
> it on your load module by readelf -h command.
>
> [WARN] xos LPG 2002 - Failed to map HugeTLBfs for data/bss: /usr/bin/uptime
>
> The e_type of elf header must be ET_EXEC when using libmpg. You can check
> it on your load module by readelf -h command.
>
> [WARN] xos LPG 2003 - Failed to map HugeTLBfs for data/bss: 

Re: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in CTAB colortable_vpnl.txt

[Huang, Yujing]

Can you check if the colortables from your install directory agree with git 
repo?
/vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt
/vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt


In your recon-all.log, there are a lot of warning messages like the following. 
I don’t know what that means.
“
[WARN] xos LPG 2002 - Failed to map HugeTLBfs for data/bss: /usr/bin/sed
The e_type of elf header must be ET_EXEC when using libmpg. You can check it on 
your load module by readelf -h command.
[WARN] xos LPG 2002 - Failed to map HugeTLBfs for data/bss: /usr/bin/uptime
The e_type of elf header must be ET_EXEC when using libmpg. You can check it on 
your load module by readelf -h command.
[WARN] xos LPG 2003 - Failed to map HugeTLBfs for data/bss: Layout problem with 
segments 0 and 1:
Segments would overlap.
“

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of LYU, TIANXIANG
Sent: Tuesday, May 7, 2024 8:36 AM
To: Freesurfer support list 
Cc: 内田航 
Subject: Re: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in 
CTAB colortable_vpnl.txt


External Email - Use Caution
Dear Yujing,

I hope this email finds you well.

I've checked the directory. /average/colortable_vpnl.txt and 
./average/colortable_BA_thresh.txt are both as the same as the ones in the git 
repo.
Also, the label files have been successfully generated in the subject’s label 
directory.
I build this freesurfer on our own aarch64 cpu, with the current source code of 
git repo. Should I try the source code of 7.4.1? which works well with its x64 
binaries on my intel-based cluster, but I'm not sure whether the problem can be 
solved on this aarch64 cpu.

Sincerely,

Tianxiang Lyu
Graduate School of Medicine,
Juntendo University

Huang, Yujing mailto:yhuan...@mgh.harvard.edu>> 
于2024年5月7日周二 21:23写道：
Your recon-all should have generated the following label files in your 
subject’s label directory:
label/?h.FG1.mpm.vpnl.label
label/?h.FG2.mpm.vpnl.label
label/?h.FG3.mpm.vpnl.label
label/?h.FG4.mpm.vpnl.label
label/?h.hOc1.mpm.vpnl.label
label/?h.hOc2.mpm.vpnl.label
label/?h.hOc3v.mpm.vpnl.label
label/?h.hOc4v.mpm.vpnl.label

I don’t know how you got your Freesurfer distributions. But it looks like your 
average/colortable_vpnl.txt is out of sync with mris_label2annot.

1. download these two colortables from Freesurfer repo - MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://github.com/freesurfer/freesurfer.git
distribution/average/colortable_BA_thresh.txt
distribution/average/colortable_vpnl.txt
2. copy them to your average/ directory

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of LYU, TIANXIANG
Sent: Tuesday, May 7, 2024 12:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: 内田航 mailto:w-uch...@juntendo.ac.jp>>
Subject: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in CTAB 
colortable_vpnl.txt


External Email - Use Caution
Hello FreeSurfer Developers,

I'm attempting to process recon-all commands, but in mris_label2annot command:

ERROR: FG1.mpm.vpnl not found in CTAB 
/vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt
Command exited with non-zero status 1
@#@FSTIME  2024:05:07:07:05:22 mris_label2annot N 26 e 4.35 S 0.34 U 2.65 P 68% 
M 203264 F 4 R 3608 W 0 c 0 w 1728 I 18304 O 0 L 0.92 0.91 0.96

I've checked the directory, but find nothing strange. (file colortable_vpnl.txt 
exists)

I've searched the list and no similar errors have been reported. Does anyone 
have any thoughts on how to trouble-shoot this one? Also, Ive attached the 
recon-all.log in case it's of any use.

Sincerely,

Tianxiang Lyu
Graduate School of Medicine,
Juntendo University
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 

Re: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in CTAB colortable_vpnl.txt

[LYU, TIANXIANG]

External Email - Use Caution

Dear Yujing,

I hope this email finds you well.

I've checked the directory. /average/colortable_vpnl.txt and
./average/colortable_BA_thresh.txt are both as the same as the ones in the
git repo.
Also, the label files have been successfully generated in the subject’s
label directory.
I build this freesurfer on our own aarch64 cpu, with the current source
code of git repo. Should I try the source code of 7.4.1? which works well
with its x64 binaries on my intel-based cluster, but I'm not sure whether
the problem can be solved on this aarch64 cpu.

Sincerely,

Tianxiang Lyu
Graduate School of Medicine,
Juntendo University

Huang, Yujing  于2024年5月7日周二 21:23写道：

> Your recon-all should have generated the following label files in your
> subject’s label directory:
>
> label/?h.FG1.mpm.vpnl.label
>
> label/?h.FG2.mpm.vpnl.label
>
> label/?h.FG3.mpm.vpnl.label
>
> label/?h.FG4.mpm.vpnl.label
>
> label/?h.hOc1.mpm.vpnl.label
>
> label/?h.hOc2.mpm.vpnl.label
>
> label/?h.hOc3v.mpm.vpnl.label
>
> label/?h.hOc4v.mpm.vpnl.label
>
>
>
> I don’t know how you got your Freesurfer distributions. But it looks like
> your average/colortable_vpnl.txt is out of sync with mris_label2annot.
>
>
>
> 1. download these two colortables from Freesurfer repo -
> https://secure-web.cisco.com/1yaJ9rtkF1pEnV3tBbwmzU19ZQQLWvibkvCE5WtM29vK2Qhee6eSfVg9hY75lhno1A0Q0zlRCN9D2we_SqyfSnlM8y0afWtm4g13yqgPYioYdjztyvi6knI0BIwx4sBnX2SY6hXES8QI1F7WNZ8NKk-H6HVwQ4LhI_6wKFlEL023LFxXzlhNLpMPl2TbPyHG_8PIMXBsXRSzfs-4t9DvHm1Z1OX8gSbHtqSvyCTbTo-_KDEaLFQmpTk6buYNbfAxhMv5_0keYI6iPJ7KZIHHjXWdgKEB_7BhnysWX6TbYYwPmizpsRsVGwlF40Ulqm46c/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer.git
>
> distribution/average/colortable_BA_thresh.txt
>
> distribution/average/colortable_vpnl.txt
>
> 2. copy them to your average/ directory
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *LYU, TIANXIANG
> *Sent:* Tuesday, May 7, 2024 12:30 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Cc:* 内田航 
> *Subject:* [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in
> CTAB colortable_vpnl.txt
>
>
>
> *External Email - Use Caution*
>
> Hello FreeSurfer Developers,
>
> I'm attempting to process recon-all commands, but in mris_label2annot
> command:
>
>
>
> ERROR: FG1.mpm.vpnl not found in CTAB
> /vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt
> Command exited with non-zero status 1
> @#@FSTIME  2024:05:07:07:05:22 mris_label2annot N 26 e 4.35 S 0.34 U 2.65
> P 68% M 203264 F 4 R 3608 W 0 c 0 w 1728 I 18304 O 0 L 0.92 0.91 0.96
>
> I've checked the directory, but find nothing strange. (file
> colortable_vpnl.txt exists)
>
>
> I've searched the list and no similar errors have been reported. Does
> anyone have any thoughts on how to trouble-shoot this one? Also, Ive
> attached the recon-all.log in case it's of any use.
>
>
>
> Sincerely,
>
>
>
> Tianxiang Lyu
>
> Graduate School of Medicine,
>
> Juntendo University
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1GzZbRd1dffTkLrKJK6QidwL9T-UH_IXj1m-sB8X0_5BL4XrS2y4CTMcsPM9YWmRI-MmfsFrxRR8RPvEwIg7dpSBAsFy7kNhLcNb52p8nA9CrteuY0vUFcjrozsqf36AgWwTRyay9vbVmtTP41juvkV9rW6M8f4UQHeelWopOsAZYJ5jeMA8cxyGhmAw7tDRJePF8nQgpAV5qvtlhltK2AhWWepEnx0U0TzX0voIvbEwRJO92ew1P278Wio06NfaxndG-NUy_3yC1MBmE3qSU2dUyhPnPQB2XMWc4PkgcUBRlmEawiSJdH1ksEB0nJhO9/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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://secure-web.cisco.com/1rc3Wcx-hUywMi198on-n_pvreKl8Pc_rh7eSQsr_yZzIpDWZeG_X6Hxqn4_Cz9dXiXZ84ZXnL6HdEX_Nt7zwCPuOhRtJPgVsCaKEcZqSXp03dy44J8l67FP6GBIPQ81ElR5c7fbk3c2-mBMcd7Jt-deTcd4TcMocTYTDAO1DUFBh94EWxZiTD2HF6sCWqooYta5GeYZWj8jcQGWwdj77dQDKlXKAfhYWRLglZkO8pxEUWsN4vogX5CdjSE-7MDdZz18LBumroQ7csnq7bS9eFRGd7tZVGLQ9RhnKaBlSyzRZULeNCSMhPAVt5905bOUa/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/1rc3Wcx-hUywMi198on-n_pvreKl8Pc_rh7eSQsr_yZzIpDWZeG_X6Hxqn4_Cz9dXiXZ84ZXnL6HdEX_Nt7zwCPuOhRtJPgVsCaKEcZqSXp03dy44J8l67FP6GBIPQ81ElR5c7fbk3c2-mBMcd7Jt-deTcd4TcMocTYTDAO1DUFBh94EWxZiTD2HF6sCWqooYta5GeYZWj8jcQGWwdj77dQDKlXKAfhYWRLglZkO8pxEUWsN4vogX5CdjSE-7MDdZz18LBumroQ7csnq7bS9eFRGd7tZVGLQ9RhnKaBlSyzRZULeNCSMhPAVt5905bOUa/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
> 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 

Re: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in CTAB colortable_vpnl.txt

[Huang, Yujing]

Your recon-all should have generated the following label files in your 
subject’s label directory:
label/?h.FG1.mpm.vpnl.label
label/?h.FG2.mpm.vpnl.label
label/?h.FG3.mpm.vpnl.label
label/?h.FG4.mpm.vpnl.label
label/?h.hOc1.mpm.vpnl.label
label/?h.hOc2.mpm.vpnl.label
label/?h.hOc3v.mpm.vpnl.label
label/?h.hOc4v.mpm.vpnl.label

I don’t know how you got your Freesurfer distributions. But it looks like your 
average/colortable_vpnl.txt is out of sync with mris_label2annot.

1. download these two colortables from Freesurfer repo - 
https://github.com/freesurfer/freesurfer.git
distribution/average/colortable_BA_thresh.txt
distribution/average/colortable_vpnl.txt
2. copy them to your average/ directory

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of LYU, TIANXIANG
Sent: Tuesday, May 7, 2024 12:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: 内田航 
Subject: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in CTAB 
colortable_vpnl.txt


External Email - Use Caution
Hello FreeSurfer Developers,

I'm attempting to process recon-all commands, but in mris_label2annot command:

ERROR: FG1.mpm.vpnl not found in CTAB 
/vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt
Command exited with non-zero status 1
@#@FSTIME  2024:05:07:07:05:22 mris_label2annot N 26 e 4.35 S 0.34 U 2.65 P 68% 
M 203264 F 4 R 3608 W 0 c 0 w 1728 I 18304 O 0 L 0.92 0.91 0.96

I've checked the directory, but find nothing strange. (file colortable_vpnl.txt 
exists)

I've searched the list and no similar errors have been reported. Does anyone 
have any thoughts on how to trouble-shoot this one? Also, Ive attached the 
recon-all.log in case it's of any use.

Sincerely,

Tianxiang Lyu
Graduate School of Medicine,
Juntendo University
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 
continue to communicate over unencrypted e-mail. 

[Freesurfer] INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE IN HEALTHCARE (AIiH)

[Jiaxiang ZHANG]

External Email - Use Caution

INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE IN HEALTHCARE (AIiH)
4 - 6 September 2024, Swansea, UK
https://secure-web.cisco.com/1ppWAnsYjYnhHxEnKoibtNl4Qu4560BMrard8EPkGQFkgmOZdkEqeqjUtjIQX2kQm8NGgSsfRBoOVu2yStRguqRu4WZNwa2kFp4I25ig4s8pwknHpKgNj5BTwefNGEtdXVXY8xqCWW3pG9XyIdRKZr3ybw_EmqAxMLBDxm71EwkN2o2RAJn95dn6B8XkSlsNxTuUQYl8vfpS5zRnCeOxDInlchDekVbzJbHa9TsEz_rDtPP-nkhjZSyhezrKXcKqxfGbsiZbiSbL8moqnzDiwl_qLyBu3gmtXhdHAdFNc51QJNd3U7gwLfOoOYLsFUGxiNIDRy6zoCLsaDl3qydpeSw/https%3A%2F%2Faiih.cc
(1st CALL FOR ABSTRACT)

[ apologies for cross-postings]

Submission deadline: Monday 1 July (FIRM)

*1. INTRODUCTION *
https://secure-web.cisco.com/1kMB0QYwXtTy8ESTcm5TslUdGzHjRontlKUqT_0F6qSbIxkzGuIQ-B9t7fASFaXGdRIn4Vk-NQGGte6yjjbS426nxf3xHow1vgz2bUFhN2yGMiOCIDTabP8Ksbm1K9WD2W5ysIcoT5zVvsq_1n82pa_llBlNdqgecePE3CwPopqNfzLFDDM543vsHpM7rZtbwXI6GqFvAPFrZ3Mp-cRfQunT949y4Iq4e4Xf69Jsf_UtaBNvCXkMV9W3qlp-v3Qk8eGeKRdYc94tZH8FvqSU691Qgtt0811ssxzZJ4uasTmH2xRiElbCDRIfpdM5jD7oxOMuW8nVVf__By57jlebubQ/https%3A%2F%2Faiih.cc%2Fabstracts%2F

AIiH 2024 welcomes late-breaking short abstract submissions to be included
as poster or short spot-light presentation at the conference. This is to
both enable fast dissemination of promising preliminary findings and
encourage attendance by a broader audience of early career researchers
(including research students), healthcare professionals, and industrial
practitioners.

AIiH 2024 is a single track conference with oral and poster presentations
and will include 5 keynote presentations. The conference will also feature
a plenary session, which consists of 3 invited speakers who have extensive
experiences in related areas.

AIiH aims to provide a prominent platform for researchers and practitioners
who are devoted to improving healthcare using modern artificial
intelligence. We recognise that healthcare applications present complex and
sometimes unique challenges across a wide spectrum, from ethics to
technical developments, that generic AI methods are often inadequate. By
creating this dedicated forum, we encourage discussions and disseminations
of efficient and effective AI solutions and technologies for healthcare,
and in turn we hope to influence the research, technology adoption, and
decision making in healthcare.


*2. KEYNOTE SPEAKERS*
https://secure-web.cisco.com/1xSHdJFsDbvhgkCBoJWdwm1K821Lxq2yKqNEYDfRAd8VVQbVJD6xOSgwi5r4erkA0NJTVmZJ1GEfJ-39_4PQS1ZjeI5MWH12d5cb8wh4dvkWgomsSH-hQyP4u0zQHRM5Qpds5Tx6mN1bPYt7QlPDY3H_Gsv2YEBnAzislePx4F0jvW-xoFOnyJk3wwkz3cJTabBDEQFTT1YWjgNJxQrPKZYu_4Pi6yTaaSdZqOvJwfoeQFCx7K-RVi2GLW71efpYYRwq2yyb_rDX1FM9wcrArfmPTfPknDpY-gV04JGV-HUs6M5ULdEq2NkW5eY2tcbIYGQuW88eke59EQJTp4WU_EQ/https%3A%2F%2Faiih.cc%2Fkeynote-speakers%2F

Prof. Hao Ni
University College London

Dr. Timothy Rittman
Cambridge University

Dr. Konstantinos Kamnitsas
Oxford University

Prof. Jacques Fleuriot
Edinburgh University

Prof. Eiichiro Tanaka
Waseda University, Japan


*3. PLENARY SESSION ON TRANSLATING AI RESEARCH INTO PRACTICE*
https://secure-web.cisco.com/154XWGvVMO2AcjTRNWbGBh-Cdh9jPWq8MlSYUd4FIqXlkR18BYS8UWws6_r5qg1AchgLm1hVElegx57HZUauaHgq6vkMnHK6k56QIbNLmm1ulXnOP5RBJKdHz2U1URUQlymIfnTLzGtW4321ywWMNGDtwTkvL4kK4_KGaU2jgRWcspYnX17-1F2htpTQawiam9U4frGztaygocR_wE7rcEc4wt1AfV8BWYLkx82HfOau32uJZAYVvqpsvInn3uNBpTu2GYKbwM8Gx5ButSX0KlMpW9O4BhzGVI9DXYaKwdddM6gHjYA-bCV4J54jPtkZiIc0cRGDiB8c_LBYgBnCaGw/https%3A%2F%2Faiih.cc%2Fplenary-session%2F

Dr. Alba Di Pardo
IRCCS Istituto Neurologico Mediterraneo Neuromed

Dr. Noura Al Moubayed
Durham University & Evergreen Life

Dr. Haoda Fu
Eli Lilly and Company


*4. ABSTRACT SUBMISSION*
Submission instructions are available at the conference website:
https://secure-web.cisco.com/1kMB0QYwXtTy8ESTcm5TslUdGzHjRontlKUqT_0F6qSbIxkzGuIQ-B9t7fASFaXGdRIn4Vk-NQGGte6yjjbS426nxf3xHow1vgz2bUFhN2yGMiOCIDTabP8Ksbm1K9WD2W5ysIcoT5zVvsq_1n82pa_llBlNdqgecePE3CwPopqNfzLFDDM543vsHpM7rZtbwXI6GqFvAPFrZ3Mp-cRfQunT949y4Iq4e4Xf69Jsf_UtaBNvCXkMV9W3qlp-v3Qk8eGeKRdYc94tZH8FvqSU691Qgtt0811ssxzZJ4uasTmH2xRiElbCDRIfpdM5jD7oxOMuW8nVVf__By57jlebubQ/https%3A%2F%2Faiih.cc%2Fabstracts%2F


*5. IMPORTANT DATES*
Abstract deadline: Monday 1 July (FIRM)
Abstract notification: Monday 8 July (FIRM)
Abstract registration: Monday 15 July
Late registration: Monday 12 August
Main conference: Wednesday 4 – Friday 6 September 2024


*5. ORGANISERS*

CONFERENCE GENERAL CHAIRS
Xianghua Xie, Swansea University, UK
Iain Styles, Queen’s University Belfast, UK

PROGRAMME CHAIRS
Gibin Powathil, Swansea University, UK
Marco Ceccarelli, University of Rome Tor Vergata, Italy

SPECIAL SESSION CHAIRS
Jiaxiang Zhang, Swansea University, UK
Rex Ying, Yale University, USA

SPONSORSHIP CHAIRS
Daniele Cafolla, Swansea University, UK
Raoul van Loon, Swansea University, UK

PUBLICITY CHAIRS
Lu Zhang, Swansea University, UK
Beiyu Lin, University of Nevada, USA

PUBLICATION CHAIR
Jingjing Deng, Durham University, UK


*6. SPONSORS*
Gold:
- Technis Blu
- Infordata
Silver:
- 

[Freesurfer] SynthSR Changes Dimension

[AmirHussein Abdolalizadeh]

External Email - Use Caution

Hi,

I'm using SynthSR on a sample of high-resolution T1 scans, however, I
noticed the dimensions are changed in between. For example, the original T1
is 176x256x256, but the SynthSRed version has a dimension of 176x257x257.

Can we resample this to the original raw scan? I noticed that the SynthSRed
version of the T1 scans is smoother and stretched in the Z-axis.

Best,
Amir
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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

[Dan Levitas]

External Email - Use Caution

Hi Kersten,

Thanks for this helpful summary. 

It seems then that it’s best to apply the threshold to the *sig.mgh file and 
visualize its results since it contains the sign that specifies the direction 
of the interaction effect. Assuming this is the case, would an appropriate 
visualization of the results in Freeview be the following?

freeview

\
-f 
$SUBJECTS_DIR/fsaverage/surf/lh.pial:overlay=lh_sig.mgh:overlay_threshold=4.4,10
 \
-f 
$SUBJECTS_DIR/fsaverage/surf/rh.pial:overlay=rh_sig.mgh:overlay_threshold=4.4,10
 \
--viewport 3d

Where the pcor value is 4.4 (pth = 0.38474), based on the LME 
spatiotemporal tutorial, including both hemispheres. This appears overly 
strict; if I go to the Configure Overlay panel in Freeview and adjust the min 
Threshold value to 97.5 % (Use percentile), I get some results. I want to 
ensure that I’m applying the correction properly. 

Thanks,

Dan

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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Understanding registration with mri_synthmorph

[Antoine Royer]

External Email - Use Caution

Hi Edward,

From my understanding, since you do not specify the registration model (the 
"-m" parameter), it assumes "-m joint", which outputs .nii.gz or .mgz; this 
explains your error message. You can use the "-m affine" parameter to allow "-t 
affine_transform.lta" and then pass it through mri_convert -at [...].

or alternatively, use the intermediate mri_warp_convert :


  1.
synthmorph -m joint (or two steps affine-deform) -t [warp.mgz]
  2.
mri_warp_convert --invox [warp.mgz] --outm3z [warp.m3z]
  3.
mri_convert -at [warp.m3z]  


Hope this helps a bit.

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de r04458...@ntu.edu.tw 

Envoyé : 5 mai 2024 02:44
À : Freesurfer support list 
Objet : Re: [Freesurfer] Understanding registration with mri_synthmorph

External Email - Use Caution

Dear Malte,

I am currently utilizing the Docker version of SynthMorph 2 for MNI
space normalization and have encountered a technical issue I hope you
can assist me with. Below, I have detailed the command line used in my
attempt:

(GBM) chang@chang-System-Product-Name:~/projects$ synthmorph -t
post_004_M_to_F.lta -T post_004_F_to_M.lta -o post_004_syn_MNI.nii.gz
-O post_004_syn_nat.nii.gz post_004_T1_nat_filled_synthsr.nii.gz
wmni_icbm152_t1_tal_nlin_asym_09c_strip.nii

I am operating SynthMorph version 2, which is sourced from Docker Hub
under the FreeSurfer user. The Docker container is managed using
/usr/bin/docker, and I have configured the /mnt directory in the image
to bind to the SUBJECTS_DIR at /home/chang/projects. The command
executed was as follows:

Running SynthMorph version 2 from 
https://secure-web.cisco.com/1HmK2M-DP5AOexQyd2JYgg54ntrZO-s0tvGJgYNHY1k6-tDOu--dgPP0ZifOOPjb1GgG64u1c5Qv0YoVym82SoKIiCdYzRC1MWsqo56OyccCl22k40XD-LidzmGTIuTVMCFjN2jyZwLQbFvh0DXT2pBoGdggjCUbSc6X-QpmDp4vmjbMSAr6wlzr0c4RG6ymeOvgD3pojUkvI4OqZtKoMSf3DKPEzNXBRRPACLxUked5a68RL1wR9V1fL3CrGZL-XPETW_EUjG_WigB99HVQUM_KPWSpL3b2PQ_RisIFaou5ZHs0HdiCe5AvoPzj407QV/https%3A%2F%2Fcan01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1Y50YTxjgoN3UdzsNhDlXNbHmFHe5Kd4HWQ6MprgqaoItzhB7TZmJmrIoLkJKt3ZcnxvmxQUCnzv0Ap54dPOiDj2bMrNyNviTT7u-iprCKXdd11a7u1TumyNiecgn-kIF08bq2J7o7t0DbgWCOgcKVJJwLfzPInBor5l_Kfc5YYoNiW8lQHAAd3KGfsRAUHv0xLTgnUfOJGRhYceU2dsqu147IhG86SLsIwt89lx7FO9S6wCrvGMs8Ab1pnP-qbpXhfFTgbH075lCeO3du_1FzBvQFtzy2Mmodedib9_BbIRvaJnEcIYy4uZin-h-B_V0%252Fhttps%25253A%25252F%25252Fhub.docker.com%25252Fu%25252Ffreesurfer%26data%3D05%257C02%257Croya2118%2540usherbrooke.ca%257C7a15aa77a7144e56d0a308dc6cceda20%257C3a5a8744593545f99423b32c3a5de082%257C0%257C0%257C638504882887527789%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3DtS2AqH%252Bh8EBtIU7cIeJ3QgDmLaVaYeXjsjnQgP0Q93I%253D%26reserved%3D0
Using /usr/bin/docker to manage containers
Will bind /mnt in image to SUBJECTS_DIR="/home/chang/projects"
Command: docker run --rm -v /home/chang/projects:/mnt -t -u 1000:1000
freesurfer/synthmorph:2
SynthMorph arguments: -t post_004_M_to_F.lta -T post_004_F_to_M.lta -o
post_004_syn_MNI.nii.gz -O post_004_syn_nat.nii.gz
post_004_T1_nat_filled_synthsr.nii.gz
wmni_icbm152_t1_tal_nlin_asym_09c_strip.nii
Traceback (most recent call last):
   File "/freesurfer/mri_synthmorph", line 608, in 
 out.save(arg.trans)
   File
"/freesurfer/env/lib/python3.11/site-packages/surfa/core/framed.py",
line 279, in save
 save_framed_array(self, filename, fmt=fmt)
   File
"/freesurfer/env/lib/python3.11/site-packages/surfa/io/framed.py",
line 137, in save_framed_array
 raise ValueError(f'cannot determine file format from extension
for {filename}')
ValueError: cannot determine file format from extension for
post_004_M_to_F.lta

Upon changing the file format from .lta to .nii.gz, the command
executed successfully. However, this adjustment presents a new
challenge as I am unable to use mri_convert to apply the
transformation to another NIfTI file.

Could you provide any insights or suggestions on how to resolve these
issues? Specifically, I need guidance on saving in the .lta format and
applying transformations using mri_convert.

Thank you in advance for your assistance.

Best regards,

-Edward
引述 "Hoffmann, Malte,PhD" :

> The displacement field stored will be the same, so I would say the
> file format shouldn't really matter. Malte
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Antoine Royer
> 
> Sent: Saturday, 

Re: [Freesurfer] Understanding registration with mri_synthmorph

[r04458005]

External Email - Use Caution

Dear Malte,

I am currently utilizing the Docker version of SynthMorph 2 for MNI  
space normalization and have encountered a technical issue I hope you  
can assist me with. Below, I have detailed the command line used in my  
attempt:

(GBM) chang@chang-System-Product-Name:~/projects$ synthmorph -t  
post_004_M_to_F.lta -T post_004_F_to_M.lta -o post_004_syn_MNI.nii.gz  
-O post_004_syn_nat.nii.gz post_004_T1_nat_filled_synthsr.nii.gz  
wmni_icbm152_t1_tal_nlin_asym_09c_strip.nii

I am operating SynthMorph version 2, which is sourced from Docker Hub  
under the FreeSurfer user. The Docker container is managed using  
/usr/bin/docker, and I have configured the /mnt directory in the image  
to bind to the SUBJECTS_DIR at /home/chang/projects. The command  
executed was as follows:

Running SynthMorph version 2 from 
https://secure-web.cisco.com/1Y50YTxjgoN3UdzsNhDlXNbHmFHe5Kd4HWQ6MprgqaoItzhB7TZmJmrIoLkJKt3ZcnxvmxQUCnzv0Ap54dPOiDj2bMrNyNviTT7u-iprCKXdd11a7u1TumyNiecgn-kIF08bq2J7o7t0DbgWCOgcKVJJwLfzPInBor5l_Kfc5YYoNiW8lQHAAd3KGfsRAUHv0xLTgnUfOJGRhYceU2dsqu147IhG86SLsIwt89lx7FO9S6wCrvGMs8Ab1pnP-qbpXhfFTgbH075lCeO3du_1FzBvQFtzy2Mmodedib9_BbIRvaJnEcIYy4uZin-h-B_V0/https%3A%2F%2Fhub.docker.com%2Fu%2Ffreesurfer
Using /usr/bin/docker to manage containers
Will bind /mnt in image to SUBJECTS_DIR="/home/chang/projects"
Command: docker run --rm -v /home/chang/projects:/mnt -t -u 1000:1000  
freesurfer/synthmorph:2
SynthMorph arguments: -t post_004_M_to_F.lta -T post_004_F_to_M.lta -o  
post_004_syn_MNI.nii.gz -O post_004_syn_nat.nii.gz  
post_004_T1_nat_filled_synthsr.nii.gz  
wmni_icbm152_t1_tal_nlin_asym_09c_strip.nii
Traceback (most recent call last):
   File "/freesurfer/mri_synthmorph", line 608, in 
 out.save(arg.trans)
   File  
"/freesurfer/env/lib/python3.11/site-packages/surfa/core/framed.py",  
line 279, in save
 save_framed_array(self, filename, fmt=fmt)
   File  
"/freesurfer/env/lib/python3.11/site-packages/surfa/io/framed.py",  
line 137, in save_framed_array
 raise ValueError(f'cannot determine file format from extension  
for {filename}')
ValueError: cannot determine file format from extension for  
post_004_M_to_F.lta

Upon changing the file format from .lta to .nii.gz, the command  
executed successfully. However, this adjustment presents a new  
challenge as I am unable to use mri_convert to apply the  
transformation to another NIfTI file.

Could you provide any insights or suggestions on how to resolve these  
issues? Specifically, I need guidance on saving in the .lta format and  
applying transformations using mri_convert.

Thank you in advance for your assistance.

Best regards,

-Edward
引述 "Hoffmann, Malte,PhD" :

> The displacement field stored will be the same, so I would say the  
> file format shouldn't really matter. Malte
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu  
>  on behalf of Antoine Royer  
> 
> Sent: Saturday, May 4, 2024 15:06
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Understanding registration with mri_synthmorph
>
> External Email - Use Caution
>
> Thanks Malte!
>
> Would you recommend anything between saving deform transforms  
> generated from synthmorph, between .mgz or .nii.gz? Which in my  
> case, are expected to be passed onto mri_warp_convert for itk  
> conversion. I'm running numerous tests trying to find  
> dissimilarities between the two approach, trying to determine which  
> will be better for me.
>
> Any insight?
> 
> De : freesurfer-boun...@nmr.mgh.harvard.edu  
>  de la part de Antoine Royer  
> 
> Envoyé : 20 avril 2024 13:52
> À : freesurfer@nmr.mgh.harvard.edu 
> Objet : Re: [Freesurfer] Understanding registration with mri_synthmorph
>
>
> External Email - Use Caution
>
> Thank you very much!!
> 
> De : freesurfer-boun...@nmr.mgh.harvard.edu  
>  de la part de Hoffmann,  
> Malte,PhD 
> Envoyé : 20 avril 2024 11:16
> À : freesurfer@nmr.mgh.harvard.edu 
> Objet : Re: [Freesurfer] Understanding registration with mri_synthmorph
>
> Hi Antoine,
>
> Thanks for reaching out. Unless you're using a dev build of  
> FreeSurfer, mri_synthmorph may lag behind the dockerized version,  
> which is likely why you see a different behavior. For affine  
> transforms, we switched to LTA format to track the source and target  
> spaces. SynthMorph now saves these with surfa, which insists on the  
> .lta suffix.
>
> Similarly, we recently added code to save warp files in .mgz format,  
> which is more similar to NIfTI and less clunky than .m3z (surfa  
> might not let you save warps with NIfTI extension just yet). Until  
> the next FS release, I would recommend using SynthMorph from the  
> Docker Hub.
>
> In any case, the warps store shifts in physical RAS space: your  
> `mri_warp_convert` call looks correct, and `antsApplyTransforms -v  
> -d 3 -i [moving] -r 

Re: [Freesurfer] Understanding registration with mri_synthmorph

[Hoffmann, Malte,PhD]

The displacement field stored will be the same, so I would say the file format 
shouldn't really matter. Malte


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Antoine Royer 

Sent: Saturday, May 4, 2024 15:06
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Understanding registration with mri_synthmorph

External Email - Use Caution

Thanks Malte!

Would you recommend anything between saving deform transforms generated from 
synthmorph, between .mgz or .nii.gz? Which in my case, are expected to be 
passed onto mri_warp_convert for itk conversion. I'm running numerous tests 
trying to find dissimilarities between the two approach, trying to determine 
which will be better for me.

Any insight?

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Antoine Royer 

Envoyé : 20 avril 2024 13:52
À : freesurfer@nmr.mgh.harvard.edu 
Objet : Re: [Freesurfer] Understanding registration with mri_synthmorph


External Email - Use Caution

Thank you very much!!

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Hoffmann, Malte,PhD 

Envoyé : 20 avril 2024 11:16
À : freesurfer@nmr.mgh.harvard.edu 
Objet : Re: [Freesurfer] Understanding registration with mri_synthmorph

Hi Antoine,

Thanks for reaching out. Unless you're using a dev build of FreeSurfer, 
mri_synthmorph may lag behind the dockerized version, which is likely why you 
see a different behavior. For affine transforms, we switched to LTA format to 
track the source and target spaces. SynthMorph now saves these with surfa, 
which insists on the .lta suffix.

Similarly, we recently added code to save warp files in .mgz format, which is 
more similar to NIfTI and less clunky than .m3z (surfa might not let you save 
warps with NIfTI extension just yet). Until the next FS release, I would 
recommend using SynthMorph from the Docker Hub.

In any case, the warps store shifts in physical RAS space: your 
`mri_warp_convert` call looks correct, and `antsApplyTransforms -v -d 3 -i 
[moving] -r [fixed] -t ants_warp.nii.gz -o out.nii.gz` should produce an image 
identical to "warped.nii.gz".

Malte


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Antoine Royer 

Sent: Friday, April 19, 2024 16:08
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Understanding registration with mri_synthmorph

External Email - Use Caution

Hi all!

I am working on implementing some freesurfer synth tools into a larger 
diffusion processing pipeline. Doing so, I would like to use mri_synthmorph to 
generate a transform and then pass it downstream. FIrstly, I use the dockerized 
synthmorph version, which seems to present discrepancies in its behaviour vs 
local testing:


  1.
Can someone explain the expected output format of freesurfer transforms? When 
used within docker, I must define affine transforms as .lta and deform 
transforms as .mgz, otherwise: "ValueError: cannot determine file format from 
extension for test__init_warp.txt"; while when using mri_synthform from my 
local freesurfer installation, it doesn't seem like an issue. While I expected 
.m3z to be the expected output.
  2.
Here is the sequence of functions I use. My objective is to pass down the 
resulting transform (affine initialization + deform warp) downstream my 
pipeline for further registration using ANTs (antsApplyTransforms). I tested 
and it seems to work, but i would appreciate an opinion. Does the --insrcgeom 
parameter fixes everything for me?

 *
Initialization + registration (freesurfer):
 *
mri_synthmorph -m affine -t  [moving] [fixed]

mri_synthmorph -m deform -t  -o  -i 
 [moving] [fixed]

Convert warp from freesurfer (RAS) to ANTs (LPS) using freesurfer warp_convert:
mri_warp_convert -g [moving] --inras  --outlps 



Thank you very much!


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Re: [Freesurfer] Understanding registration with mri_synthmorph

[Antoine Royer]

External Email - Use Caution

Thanks Malte!

Would you recommend anything between saving deform transforms generated from 
synthmorph, between .mgz or .nii.gz? Which in my case, are expected to be 
passed onto mri_warp_convert for itk conversion. I'm running numerous tests 
trying to find dissimilarities between the two approach, trying to determine 
which will be better for me.

Any insight?

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Antoine Royer 

Envoyé : 20 avril 2024 13:52
À : freesurfer@nmr.mgh.harvard.edu 
Objet : Re: [Freesurfer] Understanding registration with mri_synthmorph


External Email - Use Caution

Thank you very much!!

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Hoffmann, Malte,PhD 

Envoyé : 20 avril 2024 11:16
À : freesurfer@nmr.mgh.harvard.edu 
Objet : Re: [Freesurfer] Understanding registration with mri_synthmorph

Hi Antoine,

Thanks for reaching out. Unless you're using a dev build of FreeSurfer, 
mri_synthmorph may lag behind the dockerized version, which is likely why you 
see a different behavior. For affine transforms, we switched to LTA format to 
track the source and target spaces. SynthMorph now saves these with surfa, 
which insists on the .lta suffix.

Similarly, we recently added code to save warp files in .mgz format, which is 
more similar to NIfTI and less clunky than .m3z (surfa might not let you save 
warps with NIfTI extension just yet). Until the next FS release, I would 
recommend using SynthMorph from the Docker Hub.

In any case, the warps store shifts in physical RAS space: your 
`mri_warp_convert` call looks correct, and `antsApplyTransforms -v -d 3 -i 
[moving] -r [fixed] -t ants_warp.nii.gz -o out.nii.gz` should produce an image 
identical to "warped.nii.gz".

Malte


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Antoine Royer 

Sent: Friday, April 19, 2024 16:08
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Understanding registration with mri_synthmorph

External Email - Use Caution

Hi all!

I am working on implementing some freesurfer synth tools into a larger 
diffusion processing pipeline. Doing so, I would like to use mri_synthmorph to 
generate a transform and then pass it downstream. FIrstly, I use the dockerized 
synthmorph version, which seems to present discrepancies in its behaviour vs 
local testing:


  1.
Can someone explain the expected output format of freesurfer transforms? When 
used within docker, I must define affine transforms as .lta and deform 
transforms as .mgz, otherwise: "ValueError: cannot determine file format from 
extension for test__init_warp.txt"; while when using mri_synthform from my 
local freesurfer installation, it doesn't seem like an issue. While I expected 
.m3z to be the expected output.
  2.
Here is the sequence of functions I use. My objective is to pass down the 
resulting transform (affine initialization + deform warp) downstream my 
pipeline for further registration using ANTs (antsApplyTransforms). I tested 
and it seems to work, but i would appreciate an opinion. Does the --insrcgeom 
parameter fixes everything for me?

 *
Initialization + registration (freesurfer):
 *
mri_synthmorph -m affine -t  [moving] [fixed]

mri_synthmorph -m deform -t  -o  -i 
 [moving] [fixed]

Convert warp from freesurfer (RAS) to ANTs (LPS) using freesurfer warp_convert:
mri_warp_convert -g [moving] --inras  --outlps 



Thank you very much!


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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

[Diers, Kersten /DZNE]

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Hi Dan,

excuse the late response; regarding your remaining questions:

1)
This sounds correct to me, pcor is the corrected threshold that can be applied 
to the sig.mgh files.

2)
If I am not mistaken, the spval file should be equivalent to the sig file, at 
least for two-sided tests (the default), and with the exception that the sig 
file is at the -log10 scale and may have a sign attached to it to indicate the 
direction of effects. Since the spval file is, if I recall correctly, plain 
p-values, one could use the pth value to set a threshold for this file.
This means that we don't transform the p-values to achieve multiple comparison 
correction, but instead use a stricter threshold that controls the FDR2 at the 
0.05 level.

Best regards,

Kersten

On Thu, 2024-05-02 at 14:25 -0400, Dan Levitas wrote:
> CAUTION: This email originated from outside of DZNE. Do not click
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> beim Anklicken von Links oder Öffnen von Anhängen
>
>
> External Email - Use Caution
>
> Hi Martin,
>
> Thanks for the response!
>
> After my original post I went through things more carefully based on
> my two original two questions and made a follow-up post here
> (https://secure-web.cisco.com/19ziz4OS6HL3HuOwgHLcrspNdIovd6NTUuIdpJ-
> mDFOvCAyWs2kPDBlUfdSjbT8fclH9nL7GIu1MIetcqQwD2s6-5_CVIvLCVZ6V0NHWw83d
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> esurfer%40nmr.mgh.harvard.edu%2Fmsg76783.html) with two final
> questions. The gist of these is that I’m unsure how to apply my
> multiple comparisons (for both hemispheres) to the analysis and
> subsequent visualization. Do you have any guidance on how I should
> proceed.
>
> Much appreciated,
>
> Dan
>
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Re: [Freesurfer] recon-all process still not finishing properly

[Dong, Yilei]

External Email - Use Caution

Hi Freesurfer Developers,

Just to reply to this thread again, if I want to see if recon-all will just run 
the -fill step, do I submit it on the files that have already been run? In 
addition, does this error count as Freesurfer running out of RAM or it's more 
of a cluster issue I have to talk with the staff that manage it?

Sincerely,
Yilei

From: Dong, Yilei 
Sent: Tuesday, April 23, 2024 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] recon-all process still not finishing properly

Hi Freesurfer support,

I have several questions regarding recon-all -fill and -debug.

If we run recon-all -fill, what is the command set-up for that? From the 
ReconAllDevTable here, 
https://secure-web.cisco.com/1lmfyKn6Pvakq-RQxgJbE5k4RDGG6d0Vpvb5lGcjzph3h7UE3rIOK94h4_vGK8oa4q_FYtrbTmYfXg9SF-sFCkj4DY_oUkqnlqG_VRr6zv-uPviunfO901Vr4Llra2RZoL7k2SaVz5b8sHZwz9tr28nK4K01ItC1QwtyMTw-gA6LKU-lK3jTTjAHXqq0NK-7yqLmD6TCtsqdbNsdoxGLEfnWyV4rlB4ypTtbp8RQCkTKa8EWWLysYONW6-m24iLcIBbOt0l9i4UxjEV-DHag-8gIkxA9SeCthGdnNmHPEyy8ngikQbSR5ckvogYu-nsAi/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllDevTable,
 do we structure the recon-all command to be: recon-all -autorecon2 -fill 
-subjid ? I attempted to run recon-all -fill with -debug with the 
structure as follows: recon-all -s $subject -i $1 -fill -debug and I was 
wondering if this was the wrong format. I have also attached our 
recon-all-slurm-apr19.sb cluster submission file for reference.

Does recon-all -fill only run the fill step, while ignoring the previous steps 
before that or does recon-all run through all the initial steps including the 
-fill step ideally?

Regarding recon-all -debug, does the stdout file have the huge amounts of text 
specifying what each line is doing? I have included .out and .err files from 
the same recon-all -fill with -debug command for reference.

Sincerely,
Yilei

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

Sent: Thursday, April 18, 2024 2:57 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] recon-all process still not finishing properly

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:

External Email - Use Caution

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] surface and cortical thickness normalization

[Fischl, Bruce R.,PHD]

Hi Yunus

I think typically you would normalize by eTIV^(2/3), which would result in a 
dimensionless scaling

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of yunus soleymani
Sent: Friday, May 3, 2024 3:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] surface and cortical thickness normalization


External Email - Use Caution
Hello,

I hope you are doing well. Yesterday, I had some questions regarding 
normalization in Freesurfer. Thanks to Dr. Douglas N. Greve, I received answers 
for all of them. However, I still have one more question.

When I normalize brain surfaces to eTIV, they appear to be in two different 
units (mm2 and mm3). Will this be a problem? Additionally, I would like to know 
your thoughts on normalizing cortical thicknesses. Do you think they should be 
normalized to eTIV, or would it be better to normalize them to the mean 
cortical thickness of each subject?

I would greatly appreciate your response.

Thank you,
Yunus





Yunus Soleymani



Ph.D. Candidate of Neuroimaging

Tehran University of Medical Sciences



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[Freesurfer] surface and cortical thickness normalization

[yunus soleymani]

External Email - Use Caution

 Hello,

I hope you are doing well. Yesterday, I had some questions regarding 
normalization in Freesurfer. Thanks to Dr. Douglas N. Greve, I received answers 
for all of them. However, I still have one more question. 

When I normalize brain surfaces to eTIV, they appear to be in two different 
units (mm2 and mm3). Will this be a problem? Additionally, I would like to know 
your thoughts on normalizing cortical thicknesses. Do you think they should be 
normalized to eTIV, or would it be better to normalize them to the mean 
cortical thickness of each subject? 

I would greatly appreciate your response.

Thank you,
Yunus

Yunus
 Soleymani
Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences
soleymani.yu...@yahoo.com+98 914 526 
9298
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[Freesurfer] Difference between 2 ways to set up fsgd file and contrasts

[Lydia Chung]

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Hi FS support team,

I am going to be using mri_glmfit to test 1) main effects (which regions
show differences in cortical thickness between group 1 and group 2) and 2)
interaction effects (does the relationship between IV and DV depend on
moderator). Depending on the model, the IV is sometimes a binary
categorical variable and sometimes a continuous variable. The moderator is
always continuous. So, interaction effects are either continuous x
continuous OR categorical x continuous.

One thing I'm trying to understand is whether the two examples below are
basically two different approaches that answer the SAME question: Do people
in Group 1 differ from Group 2 on cortical thickness? Version 1 is the one
provided by FS and Version 2 is an analog of another setup I have been
provided by colleagues. Are these models answering the same or different
questions? The freesurfer link below also shows an example of how to do an
interaction (Group x Age) using Version 1 setup; for Version 2 setup of an
interaction, I know I would multiply the IV and Moderator before this step
so that I would have an additional "interaction variable" column to add as
one of the 'Variables' listed in the fsgd code.  So, I'm also curious if
the two different methods of testing an interaction (in addition to the
first question about the main effect) will get you the identical answer OR
if there is something conceptually different? Do the nuances of this setup
have to do with the difference between using DODS or DOSS?


*Main effect of Group on cortical thickness Version 1 (copied from FS
example. link here 
)*
GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
Variables Age Weight
Input subject1 Group1 30 100
Input subject2 Group2 40 120

Contrasts: 1 -1 0 0 0 0 (to test main effect of group; this feels like an
anova approach?)

*Main effect of Group on cortical thickness Version 2*
GroupDescriptorFile 1
Title OSGM
Class Subjects
Variables Group Age Weight
Input subject1 Subjects 0.5 30 100
Input subject2 Subjects -.5 40 120

contrasts: 0 1 0 0 (to test main effect of group; this feels like a linear
regression approach?)

Thank you in advance for your help!

Lydia
-- 


Lydia Wu-Chung, M.A.
Doctoral candidate
BMED Lab
Department of Psychological Sciences
Rice University
6500 Main St - MS201
Houston, TX 77030
Lab Phone: 713-348-8126
Email: lydia...@rice.edu 



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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

[Reuter, Martin,Ph.D.]

Hi Dan,

I have not worked with this code in a decade, but Kersten in my group maintains 
our  R package of it ( see https://github.com/deep-mi/fslmer ). I will bring 
this to his attention.

Basically I think you determine the joint p-threshold across hemispheres and 
convert it to FreeSurfer ( - log10 pth) and use that value as a threshold when 
plotting the original p-values. That way you only need one threshold for the 
full plot, rather than two different ones (or the more pessimistic of the two).

Also you may be interested in our whippersnappy python tool to generate nice 
looking screenshots of the surface overlay:
https://github.com/Deep-MI/whippersnappy

which is pip installable.

Best, Martin

On 2. May 2024, at 20:25, Dan Levitas  wrote:


Hi Martin,

Thanks for the response!

After my original post I went through things more carefully based on my two 
original two questions and made a follow-up post here 
(https://secure-web.cisco.com/1sMx-dupqFSyAsxsQl8ukXwR4v0-vTUkX2pc5vfwlqp166rCrDoo2bdx6p4keFMRMtTwBjqZmzCoopCuxETJGlS8kVcVUlFiUtWqouZifh-kkm5McZTXjC343IuxhPxggRZIGBfOCndTyBEfHU5yg-L0SF7Jk48ZP-_Yqg9JiZoQkXi347bobVlhhfUqU5umz6cI2eBD7bplC11HyJwUubhLdjnAYGV4QPy_JoqteaGamkmGiiirkesm6JsOmE4dUgh5w8JJfJIwHhiSus176NtxI70y9Cnc5-fIyFxbJ4NUpR41z8diD-6jjtGRt3yoMyyevPtGsNu9rgHK_-JalrQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76783.html)
 with two final questions. The gist of these is that I’m unsure how to apply my 
multiple comparisons (for both hemispheres) to the analysis and subsequent 
visualization. Do you have any guidance on how I should proceed.

Much appreciated,

Dan

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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

[Dan Levitas]

External Email - Use Caution

Hi Martin,

Thanks for the response!  

After my original post I went through things more carefully based on my two 
original two questions and made a follow-up post here 
(https://secure-web.cisco.com/19ziz4OS6HL3HuOwgHLcrspNdIovd6NTUuIdpJ-mDFOvCAyWs2kPDBlUfdSjbT8fclH9nL7GIu1MIetcqQwD2s6-5_CVIvLCVZ6V0NHWw83dN7z4bxX8JjTlz4F5ySCoY2Hn-W5BAu721AwV6QhGaqXBgr32xC1Hj1I1rKrQTyQlP1eIg9Gw3g91iL5agTdIsuQfhuCLS5fDVYGvek_rQh6ZDb-tutbyEWAlZ7ea8enpBmRCBEaMTHGC1pIKz_9aNARmcDOkjf-Znc91tyjFrHT7suqi_CYkPmpMZGFa4URHOcVwpqegNeEb-sV6X4R-YqiERw6UNMAaIXGQAFjAQ4Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76783.html)
 with two final questions. The gist of these is that I’m unsure how to apply my 
multiple comparisons (for both hemispheres) to the analysis and subsequent 
visualization. Do you have any guidance on how I should proceed.

Much appreciated,

Dan

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[Freesurfer] brain volumes normalization

[yunus soleymani]

External Email - Use Caution

Thank you for the help.my next question
When I normalize the surface area to the eTV, they are in different units (mm2, 
mm3). The resulting unit will be 1/m, is that okay?

Yunus
 Soleymani
Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences
soleymani.yu...@yahoo.com+98 914 526 
9298
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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

[Reuter, Martin,Ph.D.]

Hi Dan,

a) yes
b) yes

Best, Martin


On 22. Apr 2024, at 17:09, Dan Levitas  wrote:


Hello,

I've been following the FreeSurfer longitudinal LME analysis tutorial 
(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels),
 which has been excellent; however I have a few lingering questions pertaining 
to my specific analysis. For reference, I am interested in assessing rates of 
longitudinal atrophy in each of my two groups (0=controls, 1=clinical). 
Regarding what I've currently done:

1). My Qdec file contains 4 columns: fsid, fsid_base, time(years), group

2). I followed the steps to create the appropriate M matrix, and since my 
preliminary analysis is simply to create a group x time linear model, my design 
matrix is X = [ones(length(M),1) M M(:,1).*M(:,2)]; and my contrast is CM = [0 
0 0 1]

3). I've followed the pipeline for the lme_mass_fit_EMinit, lme_mass_RgGrow, 
and lme_mass_fit_Rgw functions.

4). I'm skipping the model comparison steps, as I prefer my model with the two 
random effects (intercept, time).

5). Get stats (F_lhstats = lme_mass_F(lhstats, CM), applied multiple comparison 
correction ([detvtx,sided_pval,pth] = 
lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0); and saved the 
sided p-values.

My questions are:

a). Since I'm interested in both hemispheres and the tutorial only assesses the 
left, do I need to do step #3 with the right hemisphere data?

b). Would I need to do the last step in the tutorial to get a single threshold 
for both hemispheres and then perform the analysis this way?

P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ];
G = [ F_lhstats.sgn(lhcortex) F_rhstats.sgn(rhcortex) ];
[detvtx,sided_pval,pth] = lme_mass_FDR2(P,G,[],0.05,0);

pcor = -log10(pth)

Thank you for the clarification.

Dan





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Re: [Freesurfer] Infant Freesufer auto-recon failure

[Zollei, Lilla,Ph.D.]

Hi Rachel,

The autorecon-pial option is not yet implemented in infant freesurfer that is 
why you see the below error.

Best, Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lemley, Rachel 

Sent: Monday, April 22, 2024 3:21 PM
To: Freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] FW: Infant Freesufer auto-recon failure


External Email - Use Caution

Good afternoon,



We are attempting to run freesurfer on infant data, but are running into an 
issue with the autorecon-pial code. We corrected the pial surface on the 
brainmask.mgz in freeview, saved the brainmask.mgz edits, and are trying to run 
autorecon-pial, but we get the following error that I have attached below. It 
is looking for a file in surf labeled lh.orig.premesh, but it does not exist. 
Any suggestions on how to fix this? Am I missing a step?



Respectfully,



Rachel Lemley







The error log is attached below:

Subject Stamp: 
freesurfer-linux-centos7_x86_64-infant-dev-4a14499-20210109-4a14499

Current Stamp: 
freesurfer-linux-centos7_x86_64-infant-dev-4a14499-20210109-4a14499

INFO: SUBJECTS_DIR is /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects

Actual FREESURFER_HOME /n/sw/ncf/apps/infant-freesurfer/4a14499/centos7_x64

Linux holy7c090602.rc.fas.harvard.edu 4.18.0-425.10.1.el8_7.x86_64 #1 SMP Thu 
Jan 12 16:32:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

'/n/sw/ncf/apps/infant-freesurfer/4a14499/centos7_x64/bin/recon-all' -> 
'/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/scripts/recon-all.local-copy'

/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri/transforms 
/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02

/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02

#

#@# Mask BFS Mon Apr 22 14:06:18 EDT 2024

/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri



mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz



threshold mask volume at 5

DoAbs = 0

Found 401939 voxels in mask (pct=  2.40)

MRImask(): AllowDiffGeom = 1

Writing masked volume to brain.finalsurfs.mgz...done.

@#@FSTIME  2024:04:22:14:06:19 mri_mask N 5 e 2.09 S 0.01 U 0.76 P 37% M 77200 
F 0 R 3233 W 0 c 64 w 51 I 768 O 768 L 2.29 1.57 1.12

@#@FSLOADPOST 2024:04:22:14:06:21 mri_mask N 5 2.29 1.57 1.12

#

#@# AutoDetGWStats lh Mon Apr 22 14:06:21 EDT 2024

cd /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri

mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i 
brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh

infant-dev-4a14499



cd /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri

setenv SUBJECTS_DIR /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects

mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i 
brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh



Reading in intensity volume brain.finalsurfs.mgz

Reading in wm volume wm.mgz

Reading in surf ../surf/lh.orig.premesh

error: No such file or directory

error: MRISread(../surf/lh.orig.premesh): could not open file

Command exited with non-zero status 1

@#@FSTIME  2024:04:22:14:06:21 mris_autodet_gwstats N 8 e 0.73 S 0.00 U 0.28 P 
39% M 43208 F 0 R 1873 W 0 c 23 w 20 I 120 O 0 L 2.29 1.57 1.12

@#@FSLOADPOST 2024:04:22:14:06:22 mris_autodet_gwstats N 8 2.29 1.57 1.12

Linux holy7c090602.rc.fas.harvard.edu 4.18.0-425.10.1.el8_7.x86_64 #1 SMP Thu 
Jan 12 16:32:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux



recon-all -s KAN1_02 exited with ERRORS at Mon Apr 22 14:06:23 EDT 2024



For more details, see the log file 
/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/scripts/recon-all.log

To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 

Re: [Freesurfer] question about infantfreesurfer

[Zollei, Lilla,Ph.D.]

Hi Knut,

The version available on the freesurfer wiki is the one that corresponds to our 
original publication. You can use it in your publication.

Lilla

From: Knut J Bjuland 
Sent: Tuesday, April 23, 2024 4:38 AM
To: freesurfer@nmr.mgh.harvard.edu ; Zollei, 
Lilla,Ph.D. 
Subject: Re: [Freesurfer] question about infantfreesurfer

External Email - Use Caution
What I mean is that it's a beta version, so I just wanted to make sure that I 
can use these results in a publication.

Knut Jørgen Bjuland
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Re: [Freesurfer] brain volumes normalization

[Douglas N. Greve]

On 5/2/2024 4:03 AM, yunus soleymani wrote:


External Email - Use Caution

Hello freesurfers,

I have some questions about the output variables of Freesurfer:

1. In the case of brain volume normalization, do I need to normalize 
all the volumetric results to the eTIV or just the subcortical volumes?

All volumes. And area too as you note in #4


2. Are there any formulas other than simple division in order to 
normalize the volumes?
People will sometimes use eTIV as a regressor in the GLM instead of 
dividing (make sure to normalize so that the scale does not mess up the GLM)


3. How are the .ThckStd values (like FS_R_Insula_ThckStd) calculated? 
What does the "std" mean here?

standard deviation across vertices


4. I believe that the surface area outputs are also affected by brain 
size differences in the population. Are there any reference values in 
the Freesurfer outputs to which surface areas can be normalized?

I just use eTIV


Thank you in advance for your help.

Best regards,
Yunus



*Yunus Soleymani*
**
*Ph.D. Candidate of Neuroimaging *
/*Tehran University of Medical Sciences*/
/**/
/*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
soleymani.yu...@yahoo.com 
/

+98 914 526 9298


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Re: [Freesurfer] Figures for publication

[Douglas N. Greve]

I would use either the ocn (cluster annotation) or the cluster-wise 
corrected map: overlay as you generally don't want to show uncorrected 
data. As for the max, it is a personal choice, just what you think looks 
good or makes your point.


On 4/22/2024 7:52 AM, Asuka Toyofuku wrote:


External Email - Use Caution

Dear Freesurfer experts,

Thanks to all the help from this community, we're finally done with 
GLM analysis(mri_glimfit) and the cluster-wise correction 
(mri_glmfit_sim), and now I'm making figures for publication.


My question is

1.
Which output mgh files are commonly used for making figures for
publication? Do people use, for example,
cache.th40.abs.sig.cluster.mgh (cluster-wise corrected map:
overlay) or cache.th40.abs.sig.masked.mgh (uncorrected sig values
masked by the clusters that survive correction) or even
uncorrected ones, such as sig.mgh file in the contrast directory
before running the correction? From my impression, not many people
use e.g., cache.th40.abs.sig.cluster.mgh (which shows no colour
gradation inside the clusters)...
2.
How do you select the colour-bar cut-off and max values? Most
publications I saw use min cut-off value: -log10(p) = 2.00 and
max: -log10(p) = 5.00, but some uses min: p=0.05 and max: p=0.01.
Obviously, if you set the max value (with the configure section)
very low (e.g., 2.0), the size of the cluster gets bigger and
looks more significant. Are there any suggestions for setting the
configure/threshold for the figures?


Many thanks,
Asuka



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[Freesurfer] brain volumes normalization

[yunus soleymani]

External Email - Use Caution

Hello freesurfers,
I have some questions about the output variables of Freesurfer:
1. In the case of brain volume normalization, do I need to normalize all the 
volumetric results to the eTIV or just the subcortical volumes?
2. Are there any formulas other than simple division in order to normalize the 
volumes?
3. How are the .ThckStd values (like FS_R_Insula_ThckStd) calculated? What does 
the "std" mean here?
4. I believe that the surface area outputs are also affected by brain size 
differences in the population. Are there any reference values in the Freesurfer 
outputs to which surface areas can be normalized?
Thank you in advance for your help.
Best regards,Yunus

Yunus
 Soleymani
Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences
soleymani.yu...@yahoo.com+98 914 526 
9298
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Re: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error

[Krystal Xiwing Yau]

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Dear FS experts,


I would like to follow up with the matter here - the T1.mgz isn't generated so 
I cannot inspect the image as instructed by the wiki page. I have checked the 
orientation on FreeView but it's correct. Would you please kindly advise?


Thank you so much. It's been grateful to have your guidance and support.


Sincerely,

Krystal


FreeSurfer Version: 7.3.2

OS: Linux on Ubuntu 23.04



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Krystal Xiwing Yau 

Sent: 29 April 2024 16:58:18
To: Freesurfer support list
Subject: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error


External Email - Use Caution

Dear FS experts,


I am encountering an error when running recon-all. I followed the FAQ 

 page to rerun the command but still not running through. Would you please 
kindly advise? The log file is attached to this email.


Thank you.


Regards,
Krystal

Tel.: +852 2255 5024
Fax: +852 2872 5828
Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.
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