Re: [Freesurfer] Transforming aseg.mgz to native anatomical space - transform files absent

[Huang, Yujing]

Hi Christine,

For the current version of Freesurfer, those transformations are in base 
directory. I don't have access to longitudinal processing using Freesurfer v6. 
Not sure when things changed.

Here is the example provided in 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat to map 
segmentation aseg to the native space:

cd $SUBJECTS_DIR/.long./mri
mri_convert -ait transforms/_to_.long..lta \
-rl $SUBJCECTS_DIR//mri/rawavg.mgz \
-rt nearest -odt uchar \
aseg.mgz aseg-in-rawavg.mgz

Replace the first line with '-ait 
$SUBJCECTS_DIR//mri/transforms/_to_.lta'.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Christine Farrugia
Sent: Thursday, September 19, 2024 11:38 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Transforming aseg.mgz to native anatomical space - 
transform files absent


External Email - Use Caution
Hi Yujing,

Many thanks for your reply.

Is this a new feature of FreeSurfer v7, then? As v6 would generate the 
_to_.long..lta files - we used that version before and I 
checked the data repository for the transformations in question.

Could you kindly advise how best to transform the aseg back to native space in 
the longitudinal case?

Christine



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: 19 September 2024 15:09
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Transforming aseg.mgz to native anatomical space - 
transform files absent

This email was sent to you by someone outside the University.
You should only click on links or attachments if you are certain that the email 
is genuine and the content is safe.

I can only find the transformations from each timepoint to base, and vice-versa 
in the base () mri/transforms directory. Those lta are used during 
long processing to transform input images to base space. I will confirm that 
and update the wiki accordingly.



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Christine Farrugia
Sent: Wednesday, September 18, 2024 9:46 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Transforming aseg.mgz to native anatomical space - 
transform files absent



External Email - Use Caution

Hi,



I'm trying to convert the aseg output of my longitudinal runs from FreeSurfer 
space back to native anatomical space by following the directions here:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat



However, I've noted that none of my subjects have a 
_to_.long..lta transformation in 
.long./mri/transforms. The transformations from each of the longs 
to the base (and vice-versa) are in the mri/transforms folder of the 
 directory, but that's about it, despite the fact that recon-all 
finished without errors. I'm using FreeSurfer v7.4.1.



Is this a feature of FreeSurfer v7 or is something going wrong somewhere?



Thanks in advance,

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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Re: [Freesurfer] BA1_exvivo does not exist in SUBJECTS_DIR fsaverage

[Huang, Yujing]

It looks like it failed to create the fsaverage symbolic link in your 
SUBJECTS_DIR.

It looks like your 
SUBJECTS_DIR=/mfs/cvl/groups/rugg/ruggdata/UTD/EXPT2/FMR/fmri102/freesurfer/ss. 
Can you check if 'fsaverage' already exits in your SUBJECTS_DIR? If so, remove 
it and re-run recon-all. Also, remove '-parallel' from recon-all command line. 
Use '-threads 4' instead.

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Sambamoorthy, Sowmya
Sent: Thursday, September 19, 2024 12:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] BA1_exvivo does not exist in SUBJECTS_DIR fsaverage


External Email - Use Caution
Hello Freesurfer support,

We have freesurfer/7.3.2 on CentOS7. This installation is working fine and the 
recons (recon-all -autorecon-pial -s $SUBJECT -parallel) run to completion.

What we are trying to do:

Upgrade OS to ROCKY Linux 8.10. and trying to make freesurfer/7.3.2 work to 
completion.The reason we are keeping 7.3.2 is to not add variance to the 
current project.

What issue we are facing: <>

Reporting on  45 segmentations
Using PrintSegStat
mri_segstats done
/mfs/cvl/groups/rugg/ruggdata/UTD/EXPT2/FMR/fmri102/freesurfer/ss/fmri102_005_rocky/label
INFO: fsaverage subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to fsaverage subject...

cd /mfs/cvl/groups/rugg/ruggdata/UTD/EXPT2/FMR/fmri102/freesurfer/ss; ln -s 
/opt/freesurfer/7.3.2/freesurfer/subjects/fsaverage; cd -

ln: failed to create symbolic link './fsaverage': File exists
#
#@# BA_exvivo Labels lh Wed Sep 11 17:06:02 CDT 2024
-
ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage!
   The fsaverage link probably points to an older freesurfer version
-
Linux rocky8-sg.cvl.utdallas.edu 4.18.0-553.8.1.el8_10.x86_64 #1 SMP Tue Jul 2 
17:10:26 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s fmri102_005_rocky exited with ERRORS at Wed Sep 11 17:06:02 CDT 
2024


More Context:

  1.  The same brain on Centos7 has no issues finishing recons. If needed, we 
can share logs for this.
  2.  We have tried adding some fsaverage switches as seen on a few support 
groups. "recon-all -autorecon-pial -s $SUBJECT -parallel --fs-subjects-dir 
$SUBJECTS_DIR". This does not seem to help and does not get past the initial 
phases of the run.

Hope this helps in giving the picture of what we are attempting to accomplish. 
Please let me know if you have any questions.

--Sowmya

Sowmya Sambamoorthy
Research Assistant
(972) 883-3746
Functional Neuroimaging of Memory Laboratory
[cid:image001.png@01DB0A97.40C8C300]
T H E   U N I V E R S I T Y   O F   T E X A S   A T   D A L L A S

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Re: [Freesurfer] Transforming aseg.mgz to native anatomical space - transform files absent

[Huang, Yujing]

I can only find the transformations from each timepoint to base, and vice-versa 
in the base () mri/transforms directory. Those lta are used during 
long processing to transform input images to base space. I will confirm that 
and update the wiki accordingly.

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Christine Farrugia
Sent: Wednesday, September 18, 2024 9:46 AM
To: Freesurfer support list 
Subject: [Freesurfer] Transforming aseg.mgz to native anatomical space - 
transform files absent


External Email - Use Caution
Hi,

I'm trying to convert the aseg output of my longitudinal runs from FreeSurfer 
space back to native anatomical space by following the directions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

However, I've noted that none of my subjects have a 
_to_.long..lta transformation in 
.long./mri/transforms. The transformations from each of the longs 
to the base (and vice-versa) are in the mri/transforms folder of the 
 directory, but that's about it, despite the fact that recon-all 
finished without errors. I'm using FreeSurfer v7.4.1.

Is this a feature of FreeSurfer v7 or is something going wrong somewhere?

Thanks in advance,
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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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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 .
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Re: [Freesurfer] [ext] Re: Question/potential bug regarding mri_convert and .gca files

[Huang, Yujing]

'mris_ca_label' will produce an annotation file - 
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label.  Is that what you are 
looking for?

The mri_convert command should work. After the conversion, you can use 
'mri_diff' to confirm they are the same.

Yujing




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Siegel, Nys Tjade
Sent: Wednesday, August 7, 2024 9:14 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [ext] Re: Question/potential bug regarding 
mri_convert and .gca files


External Email - Use Caution

Hi Bruce,



thank you for pointing out the difference between .gca and .gcs, I missed 
that...



Still, I don't manage to extract volumetric labels from the .gcs file. I've 
tried mris_convert without success, and I'm unsure whether it is the right 
command, because it is used for "converting between difference cortical surface 
file formats", whereas I would like to extract volumetric atlas labels.



I figured that /subjects/fsaverage/mri/aparc+aseg.mgz comes really close to 
what I am looking for, which is cortical labels in the volumetric space, for an 
average participant. Does that sound about right to you?



When I try to convert the aparc+aseg.mgz to a .nii file, which I could finally 
use in Python, however, the volume looks way different after the conversion 
(I'm trying mri_convert aparc+aseg.mgz ~/aparc+aseg.nii). Do I miss a flag?



Also, if there is Matlab code that helps me to extract volumetric labels from 
the .gcs file, I would gladly take it.



Best regards and much appreciation for your help,



Nys Tjade








From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>>
Sent: Monday, August 5, 2024 11:34:31 PM
To: Freesurfer support list
Subject: [ext] Re: [Freesurfer] Question/potential bug regarding mri_convert 
and .gca files


Hi Nys



.gcs is a different format for storing different information (surface-based 
parcellation) than .gca, so mri_convert won't be able to read it. There might 
be matlab code for loading .gcs files if you want. Or maybe mris_convert? I'm 
not sure, possibly someone else can take a look?



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Siegel, Nys Tjade
Sent: Monday, August 5, 2024 9:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Question/potential bug regarding mri_convert and .gca 
files



External Email - Use Caution

Dear Freesurfer community,



I'm trying to extract labels from a .gca atlas volume using the following 
command:



mri_convert atlas.gca -nth 1 labels.mgz (from 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GcaFormat)



I've found a .gca file in the /average folder for which this works 
(RB_all_2020-01-02.gca), but for the cortical parcellations I'm actually 
interested in (e.g. lh.DKTatlas40.gcs), I get the following error:



ERROR: cannot determine file type for lh.DKTatlas40.gcs

I'm pretty confused, because the documentations, as well as other support 
requests, are pretty clear on that my problem should be solved using the 
mentioned command. Notably, mri_convert -u, does not list GCA under the 
supported file-types, maybe this is a versioning issue?



I'm using freesurfer 7.2.0 with Ubunutu 22.04.4.



Any help is much appreciated.



Best regards,

Nys Tjade Siegel
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Re: [Freesurfer] Inquiry on Calculation Methods for Folding Index and Intrinsic Curvature Index in mris_anatomical_stats

[Huang, Yujing]

Here is the function that calculates the folding index and intrinsic curvature 
index of the surface - 
https://github.com/freesurfer/freesurfer/blob/dev/utils/mrisurf_metricProperties.cpp#L11335

int MRIScomputeCurvatureIndices(MRIS *mris, double *pici, double *pfi)
{
  int vno;
  VERTEX *vertex;
  double k1, k2, ici, fi, area, Kmax, Kmin;

  ici = fi = 0.0;
  for (vno = 0; vno < mris->nvertices; vno++) {
vertex = &mris->vertices[vno];
if (vertex->ripflag) {
  continue;
}
if (vno == Gdiag_no) {
  DiagBreak();
}
k1 = (double)vertex->k1;
k2 = (double)vertex->k2;
area = (double)vertex->area;
if (vertex->K > 0) {
  ici += area * (double)vertex->K;
}
Kmax = (double)fabs(k1);
Kmin = (double)fabs(k2);
fi += area * Kmax * (Kmax - Kmin);
  }

  *pfi = fi / (4.0 * M_PI);
  *pici = ici / (4.0 * M_PI);
  return (NO_ERROR);
}

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of littlepotato
Sent: Friday, August 2, 2024 5:40 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Inquiry on Calculation Methods for Folding Index and 
Intrinsic Curvature Index in mris_anatomical_stats


External Email - Use Caution

Dear FreeSurfer Support Team,
I am writing to inquire about the specific methods and formulas used by the 
mris_anatomical_stats function in Freesurfer to calculate the Folding Index and 
Intrinsic Curvature Index for each label based on annotation files.  Could you 
please provide detailed information on: the algorithms or mathematical formulas 
used to calculate the Folding Index and  Intrinsic Curvature Index for each 
label.

If there are any available documentation, publications, or example commands 
illustrating these calculations, I would greatly appreciate your sharing them.

Thank you for your assistance.

Best regards,

Amber Lin
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Re: [Freesurfer] (no subject)

[Huang, Yujing]

I’m not sure we have that option in mris_info.

If you do ‘mris_info lh.pial’, it will print vox2ras and vox2ras-tkr. You can 
compute tkrRAS to scanner RAS transformation matrix with vox2ras * 
inv(vox2ras-tkr).

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ???
Sent: Wednesday, July 17, 2024 8:18 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] (no subject)


External Email - Use Caution

​Thank you very much!

Can the transform matrix be extracted out and imported to the 3d slicer. Thus I 
can realize the registration in the slicer
-原始邮件-
发件人:"Huang, Yujing" mailto:yhuan...@mgh.harvard.edu>>
发送时间:2024-07-15 22:53:40 (星期一)
收件人: "Freesurfer support list" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
抄送:
主题: Re: [Freesurfer] (no subject)
Freesurfer lh.pial and rh.pial xyz coordinates are reported in tkregister space.

I believe you need to convert tkrRAS to RAS space using vox2ras * 
inv(vox2ras-tkr). ‘vox2ras’ and ‘vox2ras-tkr’ matrix are reported in mris_info.

If you are using Freesurfer dev version, these three TAGs (TAG_SURF_DATASPACE, 
TAG_SURF_MATRIXDATA, TAG_SURF_TRANSFORMEDSPACE) are available in the surface 
files. You can use TAG_SURF_MATRIXDATA to convert [x, y, z] coordinates between 
TAG_SURF_DATASPACE and TAG_SURF_TRANSFORMEDSPACE.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of ???
Sent: Monday, July 15, 2024 5:05 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] (no subject)


External Email - Use Caution

Dear Freesurfer Team

I have extracted the left and right cerebral cortex from the aseg.mgz file 
in the 3d slicer.

At the same time, I have loaded the lh.pial and rh.pial in the 3d slicer

the left and right cerebral cortex extracted from the aseg.mgz file was not 
in the same position with the lh.pial and rh.pial in the 3d slicer

How should I put them in the same position in the 3d slicer



Thanks

Mengjun ​​
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contains patient information, please contact the Mass General Brigham 
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] (no subject)

[Huang, Yujing]

Freesurfer lh.pial and rh.pial xyz coordinates are reported in tkregister space.

I believe you need to convert tkrRAS to RAS space using vox2ras * 
inv(vox2ras-tkr). ‘vox2ras’ and ‘vox2ras-tkr’ matrix are reported in mris_info.

If you are using Freesurfer dev version, these three TAGs (TAG_SURF_DATASPACE, 
TAG_SURF_MATRIXDATA, TAG_SURF_TRANSFORMEDSPACE) are available in the surface 
files. You can use TAG_SURF_MATRIXDATA to convert [x, y, z] coordinates between 
TAG_SURF_DATASPACE and TAG_SURF_TRANSFORMEDSPACE.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ???
Sent: Monday, July 15, 2024 5:05 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] (no subject)


External Email - Use Caution

Dear Freesurfer Team

I have extracted the left and right cerebral cortex from the aseg.mgz file 
in the 3d slicer.

At the same time, I have loaded the lh.pial and rh.pial in the 3d slicer

the left and right cerebral cortex extracted from the aseg.mgz file was not 
in the same position with the lh.pial and rh.pial in the 3d slicer

How should I put them in the same position in the 3d slicer



Thanks

Mengjun ​​
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 .
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Re: [Freesurfer] Longitudinal Analysis Error

[Huang, Yujing]

Can you check if the file exists – ‘ ls -l 
/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz’?

Can you attach the recon-all.log for both timepoints and the base processing?

Yujing





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ahmet Kaya
Sent: Wednesday, July 10, 2024 12:45 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Longitudinal Analysis Error


External Email - Use Caution
Thank you for your response. I already followed the path in the link provided 
in your email. All time points are already processed with recon-all. What I 
could see is the error is regarding that the norm.mgz can not be read, however 
I can open it with freeview.

I would appreciate your guidance on this matter.

Best,
Ahmet

On Mon, 8 Jul 2024 at 2:38 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
It looks like you are trying to create the base for two timepoints - 
‘/Applications/freesurfer/7.4.1/bin/recon-all -base 10402969_base -tp 
10402969_19 -tp 10402969_22 -all’.

I’m assuming each timepoint has been cross-sectionally processed - 
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

Best,

Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Ahmet Kaya
Sent: Sunday, July 7, 2024 9:23 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Longitudinal Analysis Error


External Email - Use Caution
Hello FreeSurfer Developers,

I am attempting to perform longitudinal analysis of brain volumes with two 
timepoints for each patient. Some of these patients were scanned using 
different scanners. When creating a base file for longitudinal analysis, I 
encounter the following error:

freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
rca-base-init 7.4.1
Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct  9 
21:32:11 PDT 2023; root:xnu-10002.41.9~7/RELEASE_ARM64_T6030 arm64
pid 3979
#
#@# Longitudinal Base Subject Creation Sat Jul  6 15:59:22 +03 2024
/Users/kayaacademia/Desktop/MS_LAB/10402969_base
\n mri_diff --notallow-pix --notallow-geo 
/Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/rawavg.mgz 
/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/rawavg.mgz \n
error: mghRead(/Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/rawavg.mgz, 
-1): could not open file
\n***
WARNING: Image parameters differ across time, maybe due to acquisition changes?
 Consistent changes in, e.g., resolution can potentially bias a
 longitudinal study! You can check image parameters by running mri_info
 on each input image. Will continue in 10 seconds ...
***\n
\n mri_robust_template --mov 
/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz 
/Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/norm.mgz --lta 
/Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/transforms/10402969_19_to_10402969_base.lta
 
/Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/transforms/10402969_22_to_10402969_base.lta
 --template 
/Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/norm_template.mgz 
--average 1 --sat 4.685 \n
7.4.1

--mov: Using /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz as 
movable/source volume.
--mov: Using /Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/norm.mgz as 
movable/source volume.
Total: 2 input volumes
--lta: Will output LTA transforms
--template: Using 
/Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/norm_template.mgz as 
template output volume.
--average: Using method 1 for template computation.
--sat: Using saturation 4.685 in M-estimator!
reading source '/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz'...
error: mghRead(/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz, 
-1): could not open file
error: MultiRegistration::loadMovables: could not open input volume 
/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz.

ERROR:
Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct  9 
21:32:11 PDT 2023; root:xnu-10002.41.9~7/RELEASE_ARM64_T6030 arm64

recon-all -s 10402969_base exited with ERRORS at Sat Jul  6 15:59:33 +03 2024



I have attached the recon-all.log file for your reference. I am not a data 
scientist and am unable to determine the cause of this issue. I would greatly 
appreciate your guidance on how to resolve this error.

  1.  FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
  2.  Platform: macOS 23.1.0
  3.  uname -a: Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 
23.1.0: Mon Oct 9 21:32:11 PDT 2023; root
.41.9~7/RELEASE_ARM64_T6030 arm64

  1.  recon-all.log: see attached

T

Re: [Freesurfer] Unknown recon-all error - ERROR: reading ../surf/autodet.gw.stats.lh.dat

[Huang, Yujing]

Can you send complete recon-all.log?  Maybe AutoDetGWStats didn’t run?

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Austin Cooper
Sent: Monday, July 8, 2024 11:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Unknown recon-all error - ERROR: reading 
../surf/autodet.gw.stats.lh.dat


External Email - Use Caution
Hello there!

I'm hoping that someone can resolve this issue which I'm having. To me it seems 
that the pipeline is looking for  ../surf/autodet.gw.stats.lh.dat, and I can 
confirm that it does not exist.

Is there a quick solution? Everything in recon-all was functioning without 
error up to this point.


The error is as follows:

mri_vol2vol done
#
#@# c2hWhiteSurfs lh Thu Jul  4 23:07:31 EDT 2024
cd 
/project/6001995/Shmuel_Mendola/data/MGH/HCPNaming/control/05_scan1/T1w/05/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg 
rawavg.aseg.presurf.mgz --wm rawavg.wm.mgz --invol rawavg.brain.finalsurfs.mgz 
--lh --i ../surf/lh.white.preaparc.rawavg --o ../surf/lh.white.rawavg --white 
--nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-wmsa --rip-surf 
../surf/lh.white.preaparc.rawavg --aparc ../label/lh.aparc.annot
ERROR: reading ../surf/autodet.gw.stats.lh.dat
ERROR:
Linux bc11246.int.ets1.calculquebec.ca 4.18.0-513.24.1.el8_9.x86_64 #1 SMP Thu 
Apr 4 18:13:02 UTC 2024 x86_64 GNU/Linux

recon-all -s 05 exited with ERRORS at Thu Jul  4 23:07:32 EDT 2024

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



Yours truly,

Austin Cooper

​BEng - University of Guelph
PBD - Cognitive Science - Carleton University
PhD Candidate - Neuroscience - McGill University
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Re: [Freesurfer] Doing math on mgz file

[Huang, Yujing]

Is this what you are looking for?

https://surfer.nmr.mgh.harvard.edu/pub/docs/wiki/mris_calc.help.xml.html


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Aaron Tanenbaum
Sent: Tuesday, July 9, 2024 2:07 PM
To: Freesurfer 
Subject: [Freesurfer] Doing math on mgz file


External Email - Use Caution
Is there an equivalent to fslmaths in freesurfer?

Thank you
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Re: [Freesurfer] Longitudinal Analysis Error

[Huang, Yujing]

It looks like you are trying to create the base for two timepoints - 
‘/Applications/freesurfer/7.4.1/bin/recon-all -base 10402969_base -tp 
10402969_19 -tp 10402969_22 -all’.

I’m assuming each timepoint has been cross-sectionally processed - 
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ahmet Kaya
Sent: Sunday, July 7, 2024 9:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal Analysis Error


External Email - Use Caution
Hello FreeSurfer Developers,

I am attempting to perform longitudinal analysis of brain volumes with two 
timepoints for each patient. Some of these patients were scanned using 
different scanners. When creating a base file for longitudinal analysis, I 
encounter the following error:

freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
rca-base-init 7.4.1
Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct  9 
21:32:11 PDT 2023; root:xnu-10002.41.9~7/RELEASE_ARM64_T6030 arm64
pid 3979
#
#@# Longitudinal Base Subject Creation Sat Jul  6 15:59:22 +03 2024
/Users/kayaacademia/Desktop/MS_LAB/10402969_base
\n mri_diff --notallow-pix --notallow-geo 
/Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/rawavg.mgz 
/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/rawavg.mgz \n
error: mghRead(/Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/rawavg.mgz, 
-1): could not open file
\n***
WARNING: Image parameters differ across time, maybe due to acquisition changes?
 Consistent changes in, e.g., resolution can potentially bias a
 longitudinal study! You can check image parameters by running mri_info
 on each input image. Will continue in 10 seconds ...
***\n
\n mri_robust_template --mov 
/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz 
/Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/norm.mgz --lta 
/Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/transforms/10402969_19_to_10402969_base.lta
 
/Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/transforms/10402969_22_to_10402969_base.lta
 --template 
/Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/norm_template.mgz 
--average 1 --sat 4.685 \n
7.4.1

--mov: Using /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz as 
movable/source volume.
--mov: Using /Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/norm.mgz as 
movable/source volume.
Total: 2 input volumes
--lta: Will output LTA transforms
--template: Using 
/Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/norm_template.mgz as 
template output volume.
--average: Using method 1 for template computation.
--sat: Using saturation 4.685 in M-estimator!
reading source '/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz'...
error: mghRead(/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz, 
-1): could not open file
error: MultiRegistration::loadMovables: could not open input volume 
/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz.

ERROR:
Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct  9 
21:32:11 PDT 2023; root:xnu-10002.41.9~7/RELEASE_ARM64_T6030 arm64

recon-all -s 10402969_base exited with ERRORS at Sat Jul  6 15:59:33 +03 2024



I have attached the recon-all.log file for your reference. I am not a data 
scientist and am unable to determine the cause of this issue. I would greatly 
appreciate your guidance on how to resolve this error.

  1.  FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
  2.  Platform: macOS 23.1.0
  3.  uname -a: Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 
23.1.0: Mon Oct 9 21:32:11 PDT 2023; root
.41.9~7/RELEASE_ARM64_T6030 arm64

  1.  recon-all.log: see attached

Thank you for your assistance, much appreciated.



Best regards,

Ahmet Kaya, MD


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Re: [Freesurfer] Calculating intensity of Individual voxel

[Huang, Yujing]

Replace [c r s] with voxel coordinates that you are interested in.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ERNEST KISSI
Sent: Tuesday, July 2, 2024 2:52 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Calculating intensity of Individual voxel


External Email - Use Caution
When I tried this , I got 0.0. I have attached a screenshot of it.


[cid:image001.png@01DACC90.A62265C0]

On Fri, Jun 21, 2024 at 2:47 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
‘mri_info vol.mgz --voxel c r s’ will print the voxel value from col row slice 
of all frames.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of ERNEST KISSI
Sent: Friday, June 21, 2024 5:16 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Calculating intensity of Individual voxel


External Email - Use Caution
Hi, freesurfer team

Is there a way to calculate the intensity of a voxel.Let say, I have a voxel 
with coordinate 20, 30 and 34 and I wanna know the intensity of it. Can it be 
done in freesurfer?
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Re: [Freesurfer] Calculating intensity of Individual voxel

[Huang, Yujing]

‘mri_info vol.mgz --voxel c r s’ will print the voxel value from col row slice 
of all frames.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ERNEST KISSI
Sent: Friday, June 21, 2024 5:16 AM
To: Freesurfer support list 
Subject: [Freesurfer] Calculating intensity of Individual voxel


External Email - Use Caution
Hi, freesurfer team

Is there a way to calculate the intensity of a voxel.Let say, I have a voxel 
with coordinate 20, 30 and 34 and I wanna know the intensity of it. Can it be 
done in freesurfer?
___
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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 
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 .
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Re: [Freesurfer] Brain in a Box

[Huang, Yujing]

Hi Hebah,

You don’t need to install Surfa separately. It is part of your Freesurfer 
installation. Surfa Volume takes .mgz/.mgh, .nii/.nii.gz formats.

Once you sourced your Freesurfer environment, use ‘fspython’ to access the 
Python distribution shipped with your Freesurfer.
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux

What I showed in previous message was from an interactive fspython session. You 
can write your own python scripts to use Surfa. On Surfa github, there are some 
documentations on how to use the library. In your sourced Freesurfer 
environment, use ‘fspython’ to run your scripts.

Best,

Yujing


From: Hebah Tanveer 
Sent: Tuesday, June 18, 2024 10:32 AM
To: Huang, Yujing 
Subject: Re: [Freesurfer] Brain in a Box


External Email - Use Caution
Hi, Yujing! I am new to the field of neuroimaging and want to better understand 
how to run Surfa. I'll need to install Python+IDE, C+IDE, and then run pip 
install surfa in my computer's command window? What is the file format of the 
slice images that Surfa will intake?

Best,
Hebah


On Tue, Jun 18, 2024 at 7:26 AM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
I'm wondering if the bbox() implementation in Surfa 
(https://github.com/freesurfer/surfa/tree/master) will achieve the task?

surfa.image.framed.bbox() 
(https://github.com/freesurfer/surfa/blob/master/surfa/image/framed.py#L203)  
computes the bounding box of the image data greater than zero.

I tried it on bert orig.mgz,

>>> import surfa as sf
>>> bert='/usr/local/freesurfer/dev/subjects/bert/mri/orig.mgz'
>>> vol=sf.load_volume(bert)
>>> vol
sf.Volume(shape=(256, 256, 256), dtype=uint8)
>>> vol.shape
(256, 256, 256)
>>> bbox=vol.bbox()
>>> bbox
(slice(47, 207, None), slice(3, 255, None), slice(3, 252, None))


Yujing

-Original Message-
From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Wighton, Paul
Sent: Monday, June 17, 2024 5:34 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Brain in a Box

Hi Hebah,

Interesting application.  You could try running mri_synthstrip then analyse the 
resulting binary mask to determine the first and last slices in each direction.

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Hebah Tanveer 
mailto:hebah.tanv...@biotexmedical.com>>
Sent: Monday, June 17, 2024 5:18 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Brain in a Box

External Email - Use Caution

I'm trying to determine the smallest rectangular prism that a brain will fit in 
based on its MRI scan. My strategy is as follows: I am moving through the brain 
axially, sagittally, and coronally to see where the brain "starts" appearing 
and "stops" appearing. Then, I'm subtracting the amount of no-brain slices from 
the total number of slices and multiplying the result by the slice thickness.

This should get me the length (sagittal plane), width (coronal plane), and 
height (axial plane) of a box that contains the brain.

Is there a function within FreeSurfer that can automate this process of 
determining "first and last sight of brain" ? It is quite time consuming to 
manually check hundreds of patients!

Best,
Hebah


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ht

Re: [Freesurfer] Brain in a Box

[Huang, Yujing]

I'm wondering if the bbox() implementation in Surfa 
(https://github.com/freesurfer/surfa/tree/master) will achieve the task?

surfa.image.framed.bbox() 
(https://github.com/freesurfer/surfa/blob/master/surfa/image/framed.py#L203)  
computes the bounding box of the image data greater than zero.

I tried it on bert orig.mgz, 

>>> import surfa as sf
>>> bert='/usr/local/freesurfer/dev/subjects/bert/mri/orig.mgz'
>>> vol=sf.load_volume(bert)
>>> vol
sf.Volume(shape=(256, 256, 256), dtype=uint8)
>>> vol.shape
(256, 256, 256)
>>> bbox=vol.bbox()
>>> bbox
(slice(47, 207, None), slice(3, 255, None), slice(3, 252, None))


Yujing

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Wighton, Paul
Sent: Monday, June 17, 2024 5:34 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Brain in a Box

Hi Hebah,

Interesting application.  You could try running mri_synthstrip then analyse the 
resulting binary mask to determine the first and last slices in each direction.

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hebah Tanveer 

Sent: Monday, June 17, 2024 5:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Brain in a Box

External Email - Use Caution

I'm trying to determine the smallest rectangular prism that a brain will fit in 
based on its MRI scan. My strategy is as follows: I am moving through the brain 
axially, sagittally, and coronally to see where the brain "starts" appearing 
and "stops" appearing. Then, I'm subtracting the amount of no-brain slices from 
the total number of slices and multiplying the result by the slice thickness.

This should get me the length (sagittal plane), width (coronal plane), and 
height (axial plane) of a box that contains the brain.

Is there a function within FreeSurfer that can automate this process of 
determining "first and last sight of brain" ? It is quite time consuming to 
manually check hundreds of patients!

Best,
Hebah


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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Re: [Freesurfer] 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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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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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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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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 .
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continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] 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<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<mailto: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<mailto: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
___
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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1GzZbRd1dffTkLrKJK6QidwL9T-UH_IXj1m-sB8X0_5BL4XrS2y4CTMcsPM9YWmRI-MmfsFrxRR8RPvEwIg7dpSBAsFy7kNhLcNb52p8nA9CrteuY0vUFcjrozsqf36AgWwTRyay9vbVmtTP41juvkV9rW6M8f4UQHeelWopOsAZYJ5jeMA8cxyGhmAw7tDRJePF8nQgpAV5qvtlhltK2AhWWepEnx0U0TzX0voIvbEwRJO92ew1P278Wio06NfaxndG-NUy_

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
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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 .
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Re: [Freesurfer] Error: Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage!

[Huang, Yujing]

$SUBJECTS_DIR/fsaverage should be symbolic link to 
$FREESURFER_HOME/subjects/fsaverage.

Can you check if it exists?

There should be lh.FG1.mpm.vpnl. label and rh.FG1.mpm.vpnl. label in 
$SUBJECTS_DIR/fsaverage/label/ directory.

What is your command?  Running the command by itself will show the help.

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Pamela González Méndez
Sent: Wednesday, April 24, 2024 9:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error: Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR 
fsaverage!


External Email - Use Caution

Hi everyone,

While running a FreeSurfer command, I encountered the following error message: 
"Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage!" This error seems 
to indicate that the specified label is missing in the fsaverage directory 
within the SUBJECTS_DIR. Any insights on resolving this issue would be 
appreciated.


Thank you!
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 .
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Problem running recon-all

[Huang, Yujing]

Is your Freesurfer Environment sourced correctly?  Here is the wiki help 
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Gregory Book
Sent: Tuesday, April 23, 2024 9:21 AM
To: freesurfer 
Subject: [Freesurfer] Problem running recon-all


External Email - Use Caution
I recently installed freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu 
22 .tar.gz). When running recon-all, I get the following error:

-bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required 
file not found

Paths are all set, and all scripts and executables have execute permissions.
What might be happening?
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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 .
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Re: [Freesurfer] Error using mris_transform in Freesurfer 7.4.1

[Huang, Yujing]

It looks like mris_transform interface changed since Freesurfer 5.3.

In Freesurfer 7.4.1, I believe you need to specify both --trx-src <> and  
--trx-dst <> if you are giving mris_transform the transform in xfm format.  Or, 
 you can use lta_convert to convert xfm to lta.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Noemí Hostalet
Sent: Tuesday, April 16, 2024 7:13 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error using mris_transform in Freesurfer 7.4.1


External Email - Use Caution
Hi,

I'm trying to run the following mris_transform command in Freesurfer version 
7.4.1:

mris_transform group1/z/Freesurfer/surf/lh.smoothwm 
group1/z/Freesurfer/mri/transforms/talairach.xfm 
group1/z/Freesurfer/surf/tal/lh.smoothwm.tal.asc

But it's giving the following error:

The transform does not have the valid src volume info.
Either you specify it with --trx-src or
make the transform to have the valid src info.

In a previous version (Freesurfer 5.3) it ran without problems.

Do you know what could be the problem?

Thank you

--
Noemí
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Re: [Freesurfer] Freeview problems

[Huang, Yujing]

I don't think you pass the arguments correctly to mri_info. You need to specify 
an input image - 'mri_info input.mgz --voxel 0 0 0'.

This should be done after you have sourced Freesurfer environment correctly. 
Here are the instructions to setup your environment on Mac 
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac

Also, which version of Freesurfer you are using?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 11:12 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problems


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Ok I tried again and when I inserted the mri_info... the output was "mri_info: 
could not parse extension from 0"

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Monday, April 15, 2024 4:44 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems


Can you try 'mri_info  --voxel 0 0 0'?   Just wanted to make sure 
the license file is read properly.



Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 10:42 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems



External Email - Use Caution

Is in the freesurfer directory



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Sent: Monday, April 15, 2024 4:40 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems



Can you confirm where your license file is?



Ruopeng



On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) 
mailto:a.sav...@student.maastrichtuniversity.nl>>
 wrote:



External Email - Use Caution

To whom it may concern,

I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), 
but freeview shuts down immediately when I try to open any file. The license is 
in the correct place.

Thank you for your help,

Best regards.

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Re: [Freesurfer] Freeview problems

[Huang, Yujing]

Can you set the terminal output?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 11:03 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problems


External Email - Use Caution
I think is not reading it properly because it gives an error, also I tried to 
setup the environment on the terminal but is not working either


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Monday, April 15, 2024 4:44 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems


Can you try 'mri_info  --voxel 0 0 0'?   Just wanted to make sure 
the license file is read properly.



Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 10:42 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems



External Email - Use Caution

Is in the freesurfer directory



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Sent: Monday, April 15, 2024 4:40 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems



Can you confirm where your license file is?



Ruopeng



On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) 
mailto:a.sav...@student.maastrichtuniversity.nl>>
 wrote:



External Email - Use Caution

To whom it may concern,

I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), 
but freeview shuts down immediately when I try to open any file. The license is 
in the correct place.

Thank you for your help,

Best regards.

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Re: [Freesurfer] Freeview problems

[Huang, Yujing]

Can you try 'mri_info  --voxel 0 0 0'?   Just wanted to make sure 
the license file is read properly.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 10:42 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview problems


External Email - Use Caution
Is in the freesurfer directory

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Sent: Monday, April 15, 2024 4:40 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems

Can you confirm where your license file is?

Ruopeng


On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) 
mailto:a.sav...@student.maastrichtuniversity.nl>>
 wrote:

External Email - Use Caution
To whom it may concern,
I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), 
but freeview shuts down immediately when I try to open any file. The license is 
in the correct place.
Thank you for your help,
Best regards.
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Re: [Freesurfer] Surface vertex tkr-ras to native T1 RAS without volume files

[Huang, Yujing]

These three TAGs (TAG_SURF_DATASPACE, TAG_SURF_MATRIXDATA, 
TAG_SURF_TRANSFORMEDSPACE) are available in the surface files if they are 
output from Freesurfer dev version.

They are the same as the metadata DataSpace/MatrixData/TransformedSpace in 
GIFTI. You can use the information to convert [x, y, z] coordinates between 
TAG_SURF_DATASPACE and TAG_SURF_TRANSFORMEDSPACE.

See freesurfer/utils/mrisurf_io.cpp:: __MRISwriteTriangularSurfaceTags() for 
implementation details.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Dipterix Wang
Sent: Thursday, April 11, 2024 10:50 AM
To: Freesurfer support list 
Subject: [Freesurfer] Surface vertex tkr-ras to native T1 RAS without volume 
files


External Email - Use Caution
Dear FreeSurfer devs,

I'm writing a program in JavaScript that converts FreeSurfer surface (mesh) 
files to other formats, which require the vertices to sit in scanner RAS 
coordinates.

Right now I'm relying on the FreeSurfer brain.finalsurf.mgz or T1.mgz file to 
obtain the Torig (vox to tkr-ras) and Norig (vox to scanner ras) matrices, and 
using these matrices to calculate the rigid transform. This approach requires 
the users to upload the mgz volume files (but I only need the transforms).

Today I found that each binary surface file (e.g. lh.pial) has a little footer 
that starts with uint32 sequence `2 0 20`, followed by the meta information 
such as xras, yras, zras, and cras. For example:

valid = 1  # volume info valid
filename = ../mri/filled-pretess127.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 1.000e+00
xras   = -1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 0.000e+00 -1.000e+00
zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = -1.000e+00 -1.700e+01 1.900e+01
\u\u\u\u0003\u\u\u\u\u\u\u0001


From what I understand, cras is the xyz of the volume center, which is the 
translation from mesh vertices xyz (in tkr-ras) to native scanner RAS.

I wonder if I can rely on this information to calculate the transform from 
tkr-ras to scan-ras, if so, where are the rotation matrices? (Affine/rigid 
transform is a 4x4 matrix, if cras is the translation, where are the first 3x3 
elements, are those always identity matrices?)

Best,
- Dipterix
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Re: [Freesurfer] recon-all exits with errors

[Huang, Yujing]

It looks like mris_fix_topology for lh hemisphere core dumped. This is from 
your recon-all.log:

“
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
Large defect found - not a problem, but a curiousity
*** stack smashing detected ***: terminated
“

In the tutorial, it has instructions on how to correct topological defects.

Also, I noticed that the recon-all was run with ‘-parallel’ option. Use 
‘-nthreads ’ instead.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of William Graves
Sent: Sunday, April 7, 2024 10:03 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all exits with errors


External Email - Use Caution
Dear FreeSurfer Developers,

I’m trying to run recon-all as a pre-processing step in the AFNI resting-state 
analysis pipline, using the command:
recon-all -subject $subj -i $anat_cm -all -parallel

So far it has successfully run on about 20 participants in my sample, but for 
the current participant it’s now suddenly throwing this error:

PIDs (691564 691567) completed and logs appended.
Linux demeter 6.2.0-26-generic #26~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Jul 
13 16:27:29 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s R21-24 exited with ERRORS at Fri Apr  5 16:29:23 EDT 2024


I searched through the log file, tried Googling the error, and searched your 
email list archive, but couldn’t find anything to address this. The log file is 
attached, along with:

1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
2) Platform: Ubuntu 22.04.3 LTS

I’d appreciate any help or advice you could give!

Best,
Will

---
William W. Graves, Ph.D.
Associate Professor, Department of Psychology
Rutgers, The State University of New Jersey
Smith Hall, Room 337
101 Warren Street, Newark, NJ  07102
http://lbbil.rutgers.edu
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Re: [Freesurfer] recon-all mri_convert error: extra argument ("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")

[Huang, Yujing]

There is a space in your path 
‘/home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe 
similar/first_sT1W_3D_TFE_tra_MR350895.nii’.

Rename the directory name and try again.

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ???
Sent: Sunday, March 31, 2024 11:18 PM
To: FreeSurfer 
Subject: [Freesurfer] recon-all mri_convert error: extra argument 
("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")


External Email - Use Caution

Hello FreeSurfer Developers,

  I'm writing to ask for help while using "recon-all" command.

  I have converted some dcm format files to to nii format. Then I ran the 
command "recon-all -s maoyipeng -i first_sT1W_3D_TFE_tra_MR350895.nii -all", an 
error appeared:

 mri_convert /home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe 
similar/first_sT1W_3D_TFE_tra_MR350895.nii 
/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz
  mri_convert: extra argument 
("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")
  type mri_convert -u for usage
  Command exited with non-zero status 1
  @#@FSTIME  2024:04:01:09:09:04 mri_convert N 3 e 0.00 S 0.00 U 0.00 P 
100% M 5972 F 0 R 236 W 0 c 0 w 1 I 0 O 0 L 0.43 0.24 0.19
  @#@FSLOADPOST 2024:04:01:09:09:04 mri_convert N 3 0.43 0.24 0.19
  Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 
00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
  recon-all -s maoyipeng exited with ERRORS at Mon Apr 1 09:09:04 HKT 2024

I've searched the list and didn't find a similar question. I'm a bit new to 
FreeSurfer, so I am unsure how to resolve this issue. I've attached the 
recon-all.log if that might help.

1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
2) uname -a: Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 
00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
3) recon-all.log: see attached


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Re: [Freesurfer] recon-all nu_correct error

[Huang, Yujing]

Hi Yilei,

I think "nu_correct: Command not found. FREESURFER: Undefined variable." is 
unrelated to your recon-all didn't finish. That error happens in the beginning 
of recon-all and recon-all uses ANTS N4BiasFieldCorrection for nu correct 
instead. We have addressed this error in our dev version.

I'm wondering if your cluster computer enforces some time, memory ... limit on 
your job.

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Dong, Yilei
Sent: Thursday, March 28, 2024 2:18 PM
To: Freesurfer support list 
Subject: [Freesurfer] recon-all nu_correct error


External Email - Use Caution
Hi Freesurfer support,


Recently, I submitted a script to run recon-all on 100 MRI images on UCSD's 
computing cluster. I get an error file that says "nu_correct: Command not 
found. FREESURFER: Undefined variable." I previously emailed this problem and 
was told to send my recon-all.log if running the recon-all did not work a 2nd 
time. I was also told previously that my cluster's Freesurfer can't locate the 
minc toolkit binaries on my system. How can this error be troubleshooted? 
Please let me know if you need any other information.



Freesurfer version: 7.2.0, but already available as module

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



Sincerely,

Yilei
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this message immediately.  Continuing to send or respond to e-mail after 
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Re: [Freesurfer] recon-all mris_preproc error: Cannot find surf/lh.w-g.pct.mgh

[Huang, Yujing]

The recon-all ‘WM/GM Contrast’ step is skipped for longitudinal base 
processing. So, I’m not sure that ‘-qcache’ option can be used in base 
processing.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Dan Levitas
Sent: Thursday, March 21, 2024 11:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all mris_preproc error: Cannot find 
surf/lh.w-g.pct.mgh


External Email - Use Caution
Hello,

I have a longitudinal dataset where each participant was scanned twice over the 
course of 5 months. I have been following FS's Longitudinal 
Tutorial.

For the CROSS section, each subjects' session scan successfully completed 
recon-all, where I used the following command:
recon-all \
-subjid sub-${sub}_ses-${ses} \
-i $raw_anat_file   \
-qcache \
-all

I then used the following recon-all command for the BASE section:
recon-all \
-base sub-${sub}_year-1 \
-tp $subjects_dir/$pre_sub_ses   \
-tp $subjects_dir/$post_sub_ses \
-qcache \
-all

This recon-all ran for several hours before failing at the following command:
mris_preproc --s sub-5009_year-1 --hemi lh --meas w-g.pct.mgh --target 
fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh

The error message is:
nsubjects = 1
ERROR: cannot find 
/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-5009_year-1/surf/lh.w-g.pct.mgh
Command exited with non-zero status 1
@#@FSTIME  2024:03:21:02:30:48 mris_preproc N 10 e 0.09 S 0.05 U 0.02 P 82% M 
3568 F 0 R 2201 W 0 c 2 w 45 I 0 O 0 L 60.94 63.09 63.23
@#@FSLOADPOST 2024:03:21:02:30:48 mris_preproc N 10 60.94 63.09 63.23
Linux 
c50.quartz.uits.iu.edu
 4.18.0-513.9.1.el8_9.x86_64 #1 SMP Thu Nov 16 10:29:04 EST 2023 x86_64 x86_64 
x86_64 GNU/Linux

recon-all -s sub-5009_year-1 exited with ERRORS at Thu Mar 21 02:30:48 EDT 2024

I have checked the archive but can't seem to find a similar question. I'm a bit 
new to FreeSurfer, so I am unsure how to resolve this issue. I've attached the 
recon-all.log if that might help.

FreeSurfer version: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460
Platform: Red Hat Enterprise Linux 8.9 Ootpa)
uname -a: Linux 
i48.red.uits.iu.edu
 4.18.0-513.9.1.el8_9.x86_64 #1 SMP Thu Nov 16 10:29:04 EST 2023 x86_64 x86_64 
x86_64 GNU/Linux
recon-all log: see attached

Thank you.

Dan

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Re: [Freesurfer] Using orig.mgz or T1.mgz as input to recon-all

[Huang, Yujing]

Not sure what went wrong in your previous run. Do you have ‘mri/orig’ directory 
under $SUBJECTS_DIR/subj? Do you have 00x.mgz in that directory?

Re-run with ‘orig.mgz’ is fine. You probably need to name the subject 
differently.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jeong Yeon Kang
Sent: Thursday, March 21, 2024 2:04 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Using orig.mgz or T1.mgz as input to recon-all


External Email - Use Caution
Hello,

Thank you for your response. I am not trying to preserve previous recon-all 
outputs, because the only outputs I have from the previous run are the orig.mgz 
and T1.mgz files.

Can I use your commands above, except with the orig.mgz file, not the 00x.mgz 
file?

If not, which options would you suggest that would get me closest to the output 
I would have gotten if I did have the raw T1s?

Thank you,
Melody

On Thu, Mar 21, 2024 at 4:51 AM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
Are you trying to preserve previous recon-all output and re-run using different 
version of Freesurfer?

If not, ‘recon-all -all -s ’ will re-run recon-all from the beginning.

You can find the original input to recon-all in mri/orig/00x.mgz. You can also 
construct new subject directory structure by copying mri/orig/00x.mgz, and run 
‘recon-all -all -s ’.

Best,

Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Jeong Yeon Kang
Sent: Wednesday, March 20, 2024 6:20 PM
To: Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Using orig.mgz or T1.mgz as input to recon-all


External Email - Use Caution
Hello FreeSurfer Developers,

I am attempting to run recon-all on a group of subjects. We no longer have the 
raw T1s. Instead, we have their orig.mgz and T1.mgz files from a previous run 
of freesurfer. We wish to rerun recon-all using their orig.mgz or T1.mgz as 
inputs, using FreeSurfer5.3. What would be the best way to go about this?

1. I ran recon-all normally, with orig.mgz as the input file. It ran to 
completion, but some files are missing from subdirectories. I am not sure if 
the outputs are correct, and comparable to other datasets that have freesurfer 
outputs that used raw T1s.

2. I converted orig.mgz to orig.nii.gz using mri_convert, and used orig.nii.gz 
as input to recon-all. This also ran to completion. However, because I cannot 
compare this output to any "true" output, I am unsure if the outputs are 
correct, and is the same as using a raw T1 as input.

3. I considered manually starting the recon process from T1.mgz (organizing 
subdirectories manually, inserting T1.mgz and orig.mgz into /mri, and starting 
autorecon2. I am unsure if this is best, as I am missing nu.mgz, which is an 
input file in the first step of autorecon2.

Please let me know what you think, and which method you think would be closest 
to using the raw T1s. I've searched the list and it seems that no one has 
attempted a similar task. Thank you.

Sincerely,
Melody
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Re: [Freesurfer] nu_correct: Command not found error

[Huang, Yujing]

You can re-run it. Send the recon-all.log if you still have problems.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Dong, Yilei
Sent: Thursday, March 21, 2024 1:26 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] nu_correct: Command not found error


External Email - Use Caution
Hi Yujing,

My recon-all just ended at that point. It didn't make it through the entire 
processing stream. Should I rerun the entire process or make any additional 
adjustments when I submit my script again?

Sincerely,
Yilei

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, March 21, 2024 6:11 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] nu_correct: Command not found error


It looks like Freesurfer can't find minc toolkit binaries on your system.



Did your recon-all finish fine? I think FS 7.2 recon-all is configured to use 
ANTS N4BiasFieldCorrection for nu correct by default.



This is from your log:

"mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 
--proto-iters 1000 --distance 50"



Best,



Yujing





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Dong, Yilei
Sent: Wednesday, March 20, 2024 2:01 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] nu_correct: Command not found error



External Email - Use Caution

Hi Freesurfer support,



Recently, I submitted a script to run recon-all on 100 mri images on UCSD's 
computing cluster, called EXPANSE. I get an error file that says "nu_correct: 
Command not found. FREESURFER: Undefined variable." The sample error file and 
the output file I have attached for one of the subjects are 
recon-all-slurm.29376886.exp-5-44.err & recon-all-slurm.29376886.exp-5-44.out 
respectively. The script I used to submit the job via slurm is called 
recon-all-slurm.sb.



I googled the error and found that someone else who had a similar situation did 
not source their Freesurfer environment correctly. Would this be the same thing 
for us as well? The main thing for us is Freesurfer/7.2.0 already has been 
available as a module for us on EXPANSE.



Sincerely,

Yilei
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Re: [Freesurfer] nu_correct: Command not found error

[Huang, Yujing]

It looks like Freesurfer can't find minc toolkit binaries on your system.

Did your recon-all finish fine? I think FS 7.2 recon-all is configured to use 
ANTS N4BiasFieldCorrection for nu correct by default.

This is from your log:
"mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 
--proto-iters 1000 --distance 50"

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Dong, Yilei
Sent: Wednesday, March 20, 2024 2:01 PM
To: Freesurfer support list 
Subject: [Freesurfer] nu_correct: Command not found error


External Email - Use Caution
Hi Freesurfer support,


Recently, I submitted a script to run recon-all on 100 mri images on UCSD's 
computing cluster, called EXPANSE. I get an error file that says "nu_correct: 
Command not found. FREESURFER: Undefined variable." The sample error file and 
the output file I have attached for one of the subjects are 
recon-all-slurm.29376886.exp-5-44.err & recon-all-slurm.29376886.exp-5-44.out 
respectively. The script I used to submit the job via slurm is called 
recon-all-slurm.sb.



I googled the error and found that someone else who had a similar situation did 
not source their Freesurfer environment correctly. Would this be the same thing 
for us as well? The main thing for us is Freesurfer/7.2.0 already has been 
available as a module for us on EXPANSE.



Sincerely,

Yilei
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Re: [Freesurfer] Using orig.mgz or T1.mgz as input to recon-all

[Huang, Yujing]

Are you trying to preserve previous recon-all output and re-run using different 
version of Freesurfer?

If not, ‘recon-all -all -s ’ will re-run recon-all from the beginning.

You can find the original input to recon-all in mri/orig/00x.mgz. You can also 
construct new subject directory structure by copying mri/orig/00x.mgz, and run 
‘recon-all -all -s ’.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jeong Yeon Kang
Sent: Wednesday, March 20, 2024 6:20 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using orig.mgz or T1.mgz as input to recon-all


External Email - Use Caution
Hello FreeSurfer Developers,

I am attempting to run recon-all on a group of subjects. We no longer have the 
raw T1s. Instead, we have their orig.mgz and T1.mgz files from a previous run 
of freesurfer. We wish to rerun recon-all using their orig.mgz or T1.mgz as 
inputs, using FreeSurfer5.3. What would be the best way to go about this?

1. I ran recon-all normally, with orig.mgz as the input file. It ran to 
completion, but some files are missing from subdirectories. I am not sure if 
the outputs are correct, and comparable to other datasets that have freesurfer 
outputs that used raw T1s.

2. I converted orig.mgz to orig.nii.gz using mri_convert, and used orig.nii.gz 
as input to recon-all. This also ran to completion. However, because I cannot 
compare this output to any "true" output, I am unsure if the outputs are 
correct, and is the same as using a raw T1 as input.

3. I considered manually starting the recon process from T1.mgz (organizing 
subdirectories manually, inserting T1.mgz and orig.mgz into /mri, and starting 
autorecon2. I am unsure if this is best, as I am missing nu.mgz, which is an 
input file in the first step of autorecon2.

Please let me know what you think, and which method you think would be closest 
to using the raw T1s. I've searched the list and it seems that no one has 
attempted a similar task. Thank you.

Sincerely,
Melody
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mri_label2vol fillribbon issue

[Huang, Yujing]

Hi Letitia,

Can you send the full command lines that you ran and the output?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Schneider, Letitia Maria
Sent: Thursday, March 14, 2024 10:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_label2vol fillribbon issue


External Email - Use Caution
Hello,

I am using Freesurfer version 7.3.2 on a mac.
I am using the mri_label2vol function to project an anatomical label into 
volume space, but I realised the label comes out wrong when I use the 
--fill-ribbon flag: its orientation changes to RSP.
The same label comes out right when I use the --fillthresh flag (oriented in 
RPI).
Any idea why using --fillribbon changes the orientation?

Thank you in advance.

Best wishes,
Letitia
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 .
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area

[Huang, Yujing]

[​Folder icon] 
https://partnershealthcare-my.sharepoint.com/:f:/g/personal/yhuang43_mgh_harvard_edu/EpPzvvFe_jJFvpRs1gHUEwcB_z1zoKX_V0KktTrtGvHklw?email=taylor.ariko%40miami.edu&e=nQS1oZ

I uploaded those two binaries to OneDrive. Let me know if you can access them.


From: Huang, Yujing
Sent: Tuesday, March 12, 2024 2:55 PM
To: 'Freesurfer support list' 
Subject: RE: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area

Hi Taylor,

Attached are mri_info and mris_calc from our dev version for Darwin-x86-64. 
Make a copy of your current binaries, and copy them into your 
$FREESURFER_HOME/bin. Make sure they have the execute permission.

Let me know how they work for you!

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Ariko, Taylor
Sent: Tuesday, March 12, 2024 9:53 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area


External Email - Use Caution
That would be wonderful, thank you.

Best,
Taylor

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>
Date: Thursday, March 7, 2024 at 9:05 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area
Yujing, you can just send Taylor a binary that can be put in the local version 
of $FREESURFER/bin
On 3/6/2024 11:45 AM, Huang, Yujing wrote:
Hi Taylor,

Thanks for sharing the data.

I see the problem now.  The first 14336 bytes of your rh.area fit SIGNA_FILE 
criteria. So, it is read as SIGNA_FILE instead of MRI_CURV_FILE.

We will have a fix in dev version. But I’m not sure how to get around this in 
FS 7.2.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 On Behalf Of Ariko, Taylor
Sent: Wednesday, March 6, 2024 9:47 AM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area


External Email - Use Caution
Hello Yujing,


If I rerun this command:

mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

It says it is writing curvature file in the command line output:

writing curvature file ../surf/rh.area

Though the problem persists (mri_info says same thing as before). I have 
attached rh.white and rh.area for your review.


Many thanks,
Taylor



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Wednesday, March 6, 2024 at 8:37 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area
It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should 
show it is a ‘curv’ file with nvertices x 1 x 1 dimensions.

I’m not sure where exactly the area values are calculated. What happen if you 
re-run this step?
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

Can you share the ?h.white and ?h.area?

Best,

Yujing







From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Ariko, Taylor
Sent: Tuesday, March 5, 2024 7:24 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area


External Email - Use Caution
Hello Yujing,


Thank you for your quick response!


When I run:

mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add 
/path/to/subject/surf/rh.area.pial

I get the following error:

error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not 
open file
error: No such file or directory
error:
mris_calc: could not establish read access to 
'/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.


But when I run:

mri_info rh.area

I get the following output:

Volume information for rh.area
  type: unknown
dimensions: 831 x 10015 x 25953
   voxel sizes: -0.00, -0.00,nan
  type: SHORT (4)
   

Re: [Freesurfer] ascii: bad interpreter: No such file or directory

[Huang, Yujing]

Hi Brian,

Since there is no output, I’m wondering if it passed reading lh.cortex.label.

Some questions:
1. how did you generate lh.cortex.label? It needs to have the format described 
here - https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles
2. what is your SUBJECTS_DIR?  ‘echo $SUBJECTS_DIR’ will show it.
3. can you try adding ‘-seed 1234’ option to your command line?
 Make sure to add it after ‘-l ’. I just wanted to 
confirm if mris_ca_label read your lh.cortex.label correctly. It should print 
‘setting seed for random number generator to 1234’ if lh.cortex.label is read 
fine.
4. I noticed that you have ‘sub-004’ in the path to lh.cortex.label, but the 
subject id passed to mris_ca_label is ‘001’.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Kavanaugh, Brian
Sent: Wednesday, March 6, 2024 5:41 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory


External Email - Use Caution
Thanks again Yujing.

There is not, here is a screen shot of the command (I removed the other inputs 
for clarity) followed by the output, which is just "segmentation fault (core 
dumped)"

[cid:image001.png@01DA7077.5F9EC230]

I think before you asked which free surfer version, which is here:

[cid:image002.png@01DA7077.5F9EC230]

On Wed, Mar 6, 2024 at 4:51 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
It is hard to tell without the data. Is there any output before the core dump?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Sennott, Liam Ricker
Sent: Wednesday, March 6, 2024 4:28 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory

Sending on behalf of Brian who was having trouble sending a reply:


Dear Yujing,

Thank you! Haha yes, a silly error there with the -1/-l.

When I correctly put -l, I now get the following error: "segmentation fault 
core dumped". Might this error make any sense to you?

Brian


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Wednesday, March 6, 2024 at 11:05 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory
Sorry, just recognized it. The option to pass label file is ‘-l’.  It looks 
like you have ‘-1’ instead.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Wednesday, March 6, 2024 10:57 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory

I’m not sure which version of Freesurfer you are using. But it seems the 
command line options are not in the right order.  Here is the wiki help - 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label<https://secure-web.cisco.com/1mpplmqgALrQMWIYrLdz3-T81mClV9RLqIm7McPPGsKuRnj2GZ84HFV-m2wmxmkJ5F593L8IKHZ6sZ0aXD-oWhfy15Bp_Xd7OwdkVBmvVpSKi8WWDeqld0BFIAoDNKizWPhuE2G5HuZftvudh-oEvUhJcnqegcfT3_TP3ZKvuoIidvkW5WDXhEmzC8X_Qo_Hs3sR3msa2y9vowhXlfwNWiuswFZpnOye-0L2s3kPrbLeG9zsuTUy_ti2vaoEgrbTLEZfbCmM4pyT0SpKTovARJbhi48KwmGxudsIgYOh6QRGNps6NRKE4ji8J2aOK0SQ_Pgx40qIepWK3rUepCcTJ6g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_ca_label>

Best,

Yujing


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Kavanaugh, Brian
Sent: Wednesday, March 6, 2024 8:55 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] ascii: bad interpreter: No such file or directory


External Email - Use Caution
Hello everyone,

I am new to freesurfer so I apologize if this is a simple answer.

i'm running mris_ca_label to get the BN atlas parcellation:

mris_ca_label -1
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.cortex.label
 001 lh
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/surf/lh.sphere.reg
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/lh.BN_Atlas.gcs
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.BN_Atlas.annot

But it seems freesurfer is having an issue reading my lh.cortex.label file:
/users/bkavanau/data/bkavanau/temp/deriva

Re: [Freesurfer] ascii: bad interpreter: No such file or directory

[Huang, Yujing]

It is hard to tell without the data. Is there any output before the core dump?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Sennott, Liam Ricker
Sent: Wednesday, March 6, 2024 4:28 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory

Sending on behalf of Brian who was having trouble sending a reply:


Dear Yujing,

Thank you! Haha yes, a silly error there with the -1/-l.

When I correctly put -l, I now get the following error: "segmentation fault 
core dumped". Might this error make any sense to you?

Brian


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Wednesday, March 6, 2024 at 11:05 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory
Sorry, just recognized it. The option to pass label file is ‘-l’.  It looks 
like you have ‘-1’ instead.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Wednesday, March 6, 2024 10:57 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory

I’m not sure which version of Freesurfer you are using. But it seems the 
command line options are not in the right order.  Here is the wiki help - 
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label

Best,

Yujing


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Kavanaugh, Brian
Sent: Wednesday, March 6, 2024 8:55 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] ascii: bad interpreter: No such file or directory


External Email - Use Caution
Hello everyone,

I am new to freesurfer so I apologize if this is a simple answer.

i'm running mris_ca_label to get the BN atlas parcellation:

mris_ca_label -1
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.cortex.label
 001 lh
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/surf/lh.sphere.reg
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/lh.BN_Atlas.gcs
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.BN_Atlas.annot

But it seems freesurfer is having an issue reading my lh.cortex.label file:
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.cortex.label:
 ascii: bad interpreter: No such file or directory

Might anyone have thoughts on how to resolve? I've seen adjacent errors before, 
but none related to ascii specifically.

thank you!

brian

Brian Kavanaugh, PsyD, ABPP
Board Certified Pediatric Neuropsychologist, E. P. Bradley Hospital
Assistant Professor, Warren Alpert Medical School of Brown University
___
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The information in this e-mail is intended only for the person to whom it is 
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Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area

[Huang, Yujing]

Hi Taylor,

Thanks for sharing the data.

I see the problem now.  The first 14336 bytes of your rh.area fit SIGNA_FILE 
criteria. So, it is read as SIGNA_FILE instead of MRI_CURV_FILE.

We will have a fix in dev version. But I’m not sure how to get around this in 
FS 7.2.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ariko, Taylor
Sent: Wednesday, March 6, 2024 9:47 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area


External Email - Use Caution
Hello Yujing,


If I rerun this command:

mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

It says it is writing curvature file in the command line output:

writing curvature file ../surf/rh.area

Though the problem persists (mri_info says same thing as before). I have 
attached rh.white and rh.area for your review.


Many thanks,
Taylor



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Wednesday, March 6, 2024 at 8:37 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area
It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should 
show it is a ‘curv’ file with nvertices x 1 x 1 dimensions.

I’m not sure where exactly the area values are calculated. What happen if you 
re-run this step?
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

Can you share the ?h.white and ?h.area?

Best,

Yujing







From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Ariko, Taylor
Sent: Tuesday, March 5, 2024 7:24 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area


External Email - Use Caution
Hello Yujing,


Thank you for your quick response!


When I run:

mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add 
/path/to/subject/surf/rh.area.pial

I get the following error:

error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not 
open file
error: No such file or directory
error:
mris_calc: could not establish read access to 
'/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.


But when I run:

mri_info rh.area

I get the following output:

Volume information for rh.area
  type: unknown
dimensions: 831 x 10015 x 25953
   voxel sizes: -0.00, -0.00,nan
  type: SHORT (4)
   fov: 1016.473
   dof: 1
xstart: 0.0, xend: 990983162970892849632569550308376576.0
ystart: -0.0, yend: 3079152361728581627851833344.0
zstart: -0.0, zend: -3815443229699337177012458129513775104.0
TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 
-18770011487391973376.
  : x_a =   0., y_a =   0., z_a =   1., c_a =nan
  : x_s =   0., y_s =  -1., z_s =   0., c_s =-0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
0.  -0.  nannan
   -0.  -0.  nannan
   -0.   0.  nannan
0.   0.   0. 1.

voxel-to-ras determinant nan

ras to voxel transform:
error: mat = NULL!


It appears that this is where the issue is coming from. Any ideas on why this 
is occurring? The brain is normal and has good rh.white and rh.pial surfaces.


Many thanks,
Taylor


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Tuesday, March 5, 2024 at 4:25 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not 
establish read access to rh.area
CAUTION: This email originated from outside the organization. DO NOT CLICK ON 
LINKS or OPEN ATTACHMENTS unless you know and trust the sender.
Hi Taylor,

I don’t understand how you could get that error.  It seems to me that 
read_signa() is for reading .signa files.

Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ directly? Pass 
full path to your rh.area and rh.area.pial.

What does ‘mri_info rh.

Re: [Freesurfer] ascii: bad interpreter: No such file or directory

[Huang, Yujing]

Sorry, just recognized it. The option to pass label file is ‘-l’.  It looks 
like you have ‘-1’ instead.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Wednesday, March 6, 2024 10:57 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory

I’m not sure which version of Freesurfer you are using. But it seems the 
command line options are not in the right order.  Here is the wiki help - 
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label

Best,

Yujing


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Kavanaugh, Brian
Sent: Wednesday, March 6, 2024 8:55 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] ascii: bad interpreter: No such file or directory


External Email - Use Caution
Hello everyone,

I am new to freesurfer so I apologize if this is a simple answer.

i'm running mris_ca_label to get the BN atlas parcellation:

mris_ca_label -1
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.cortex.label
 001 lh
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/surf/lh.sphere.reg
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/lh.BN_Atlas.gcs
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.BN_Atlas.annot

But it seems freesurfer is having an issue reading my lh.cortex.label file:
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.cortex.label:
 ascii: bad interpreter: No such file or directory

Might anyone have thoughts on how to resolve? I've seen adjacent errors before, 
but none related to ascii specifically.

thank you!

brian

Brian Kavanaugh, PsyD, ABPP
Board Certified Pediatric Neuropsychologist, E. P. Bradley Hospital
Assistant Professor, Warren Alpert Medical School of Brown 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 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] ascii: bad interpreter: No such file or directory

[Huang, Yujing]

I’m not sure which version of Freesurfer you are using. But it seems the 
command line options are not in the right order.  Here is the wiki help - 
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Kavanaugh, Brian
Sent: Wednesday, March 6, 2024 8:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ascii: bad interpreter: No such file or directory


External Email - Use Caution
Hello everyone,

I am new to freesurfer so I apologize if this is a simple answer.

i'm running mris_ca_label to get the BN atlas parcellation:

mris_ca_label -1
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.cortex.label
 001 lh
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/surf/lh.sphere.reg
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/lh.BN_Atlas.gcs
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.BN_Atlas.annot

But it seems freesurfer is having an issue reading my lh.cortex.label file:
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.cortex.label:
 ascii: bad interpreter: No such file or directory

Might anyone have thoughts on how to resolve? I've seen adjacent errors before, 
but none related to ascii specifically.

thank you!

brian

Brian Kavanaugh, PsyD, ABPP
Board Certified Pediatric Neuropsychologist, E. P. Bradley Hospital
Assistant Professor, Warren Alpert Medical School of Brown 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. 

Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area

[Huang, Yujing]

It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should 
show it is a ‘curv’ file with nvertices x 1 x 1 dimensions.

I’m not sure where exactly the area values are calculated. What happen if you 
re-run this step?
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

Can you share the ?h.white and ?h.area?

Best,

Yujing







From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ariko, Taylor
Sent: Tuesday, March 5, 2024 7:24 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area


External Email - Use Caution
Hello Yujing,


Thank you for your quick response!


When I run:

mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add 
/path/to/subject/surf/rh.area.pial

I get the following error:

error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not 
open file
error: No such file or directory
error:
mris_calc: could not establish read access to 
'/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.


But when I run:

mri_info rh.area

I get the following output:

Volume information for rh.area
  type: unknown
dimensions: 831 x 10015 x 25953
   voxel sizes: -0.00, -0.00,nan
  type: SHORT (4)
   fov: 1016.473
   dof: 1
xstart: 0.0, xend: 990983162970892849632569550308376576.0
ystart: -0.0, yend: 3079152361728581627851833344.0
zstart: -0.0, zend: -3815443229699337177012458129513775104.0
TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 
-18770011487391973376.
  : x_a =   0., y_a =   0., z_a =   1., c_a =nan
  : x_s =   0., y_s =  -1., z_s =   0., c_s =-0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
0.  -0.  nannan
   -0.  -0.  nannan
   -0.   0.  nannan
0.   0.   0. 1.

voxel-to-ras determinant nan

ras to voxel transform:
error: mat = NULL!


It appears that this is where the issue is coming from. Any ideas on why this 
is occurring? The brain is normal and has good rh.white and rh.pial surfaces.


Many thanks,
Taylor


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Tuesday, March 5, 2024 at 4:25 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not 
establish read access to rh.area
CAUTION: This email originated from outside the organization. DO NOT CLICK ON 
LINKS or OPEN ATTACHMENTS unless you know and trust the sender.
Hi Taylor,

I don’t understand how you could get that error.  It seems to me that 
read_signa() is for reading .signa files.

Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ directly? Pass 
full path to your rh.area and rh.area.pial.

What does ‘mri_info rh.area’ report?

Best,

Yujing


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Ariko, Taylor
Sent: Tuesday, March 5, 2024 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read 
access to rh.area


External Email - Use Caution
Hello FreeSurfer Developers,


I am attempting to run the recon-all pipeline on one subject using the 
following code:

recon-all -all -i t1.nii -s p03_1

Although, I get the following error in the command line:

mris_calc -o rh.area.mid rh.area add rh.area.pial
error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not 
open file
error: No such file or directory
error:
mris_calc: could not establish read access to 'rh.area'.

Tue Aug  1 15:58:13 EDT 2023
ERROR: vertexvol
mris_calc -o rh.area.mid rh.area add rh.area.pial
Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul  5 
22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64

recon-all -s p03_8 exited with ERRORS at Tue Aug  1 15:58:13 EDT 2023

To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<https://secure-web.cisco.com/1jPGfvEBFLG40bsU54UXs7wMCIp3C8zH7DpuFNxTMYcjl-sV

Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area

[Huang, Yujing]

Hi Taylor,

I don't understand how you could get that error.  It seems to me that 
read_signa() is for reading .signa files.

Can you try 'mris_calc -o rh.area.mid rh.area add rh.area.pial' directly? Pass 
full path to your rh.area and rh.area.pial.

What does 'mri_info rh.area' report?

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ariko, Taylor
Sent: Tuesday, March 5, 2024 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read 
access to rh.area


External Email - Use Caution
Hello FreeSurfer Developers,


I am attempting to run the recon-all pipeline on one subject using the 
following code:

recon-all -all -i t1.nii -s p03_1

Although, I get the following error in the command line:

mris_calc -o rh.area.mid rh.area add rh.area.pial
error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not 
open file
error: No such file or directory
error:
mris_calc: could not establish read access to 'rh.area'.

Tue Aug  1 15:58:13 EDT 2023
ERROR: vertexvol
mris_calc -o rh.area.mid rh.area add rh.area.pial
Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul  5 
22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64

recon-all -s p03_8 exited with ERRORS at Tue Aug  1 15:58:13 EDT 2023

To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

The recon-all.error file contains:

--
SUBJECT p03_8
DATE Tue Aug  1 15:58:13 EDT 2023
USER taylorariko
HOST C02F10PVPN5W.local
PROCESSOR x86_64
OS Darwin
Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul  5 
22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b)
/Applications/freesurfer/7.2.0/bin/recon-all
PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri
CMD vertexvol --s p03_8 --rh --th3

I have made sure that I have read, write, and execute access to the folder 
/path/to/subject/surf and the file rh.area. I can successfully run the command 
to make rh.area (mris_place_surface --area-map ../surf/rh.white 
../surf/rh.area), but the error persists in using rh.area. I have disk space 
and can run other commands such as this fake one (mris_calc -o rh.area.Test 
rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to 
rerun the command from root and get the same error message.

I found 2 similar threads of the mail-archive, though I didn't find any 
remedies:

  1.  MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg44230.html
  2.  MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51444.html

Does anyone have any thoughts on how to trouble-shoot this? I have included my 
recon-all.log in the case it is of any use.


  1.  Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
  2.  Platform: macOS Sonoma 14.3.1
  3.  uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: 
Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64
  4.  recon-all.log: see attached


Thanks in advance!

Taylor Ariko

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The informatio

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

[Huang, Yujing]

1. 'mris_convert' uses the metadata 'AnatomicalStructurePrimary' value in 
surface gii to determine the left/right hemi
grep -A 2 -B 1 'AnatomicalStructurePrimary' surf/lh.white.gii
 


 

2. I think the error that you get from 'mri_aparc2aseg' is because the .annot 
is for fsaverage not the individual subject surface. I think you can use 
mri_surf2surf to generate .annot in individual surface space - 
https://freesurfer.net/fswiki/mri_surf2surf

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 5:55 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?


External Email - Use Caution

Hi again and sorry for the very confusing questions...



I now (without really knowing what I did) managed to get

mris_convert --annot left.fsaverage_MY_PARC_2_164.label.gii 
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii 
lh.MY_PARC_164k_1.annot

to run without errors. However it creates an .annot file with a rh.lh -prefix, 
eg rh.lh.MY_PARC_164k_1.annot

I've checked multiple times that the .label.gii file used as input is really 
Left Hemisphere. I tried just renaming the .annot file but then

mri_aparc2aseg --old-ribbon --s subject --annot MY_PARC_164k_1 --o 
MY_PARC_164k_1.mgz

gives the following error


Loading lh annotations from ~/subjects_dir/subject/label/lh.MY_PARC_164k_1.annot
error: No such file or directory
error: # elements (163842) in 
~/subjects_dir/subject/label/lh.MY_PARC_164k_1.annot and # vertices (154818) 
don't match
ERROR: MRISreadAnnotation() failed 
~/subjects_dir/subject/label/lh.MY_PARC_164k_1.annot

best and thanks for the help

karin


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, February 29, 2024 10:59:50 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

All these filenames are too similar. You mentioned at least 3 different files.

mris_info 
fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii (error)
mris_info 
fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii(ok)
mris_convert 
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii (error)
ls -lt   
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii  (ok)

Make sure the file exists and provide full path to mris_info/mris_convert 
command.

If you continue to have problems with mris_info/mris_convert, share the .gii 
and we will take a closer look.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 4:41 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?


External Email - Use Caution

Hi again this gives


ls -lt fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
-rw-rw-r-- 1 karin karin 4323015 feb 29 21:54 
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
best

karin


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, February 29, 2024 10:29:25 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

It seems to me that it failed to open the .gii file.

Can you check if 
'fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii' exists and you 
have the read permission?
'ls -lt fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii'



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 4:09 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?


External Email - Use Caution

Hi I realized that the error occurs only with the Lh- file, that also gives 
this error


mris_info fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
** failed to open GIFTI XML file 
'fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii'
gifti_read_image() returned NULL

Is this a freesurfer error or i

Re: [Freesurfer] lack of volume called 001.mgz

[Huang, Yujing]

I'm not sure what files you copied over. For the initial run of recon-all, you 
need to specify input files using '-i ' option. See recon-all wiki 
help page for detail: 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Best,

Yujing


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Joanna Kidon
Sent: Saturday, March 2, 2024 1:37 PM
To: Freesurfer support list 
Subject: [Freesurfer] lack of volume called 001.mgz

External Email - Use Caution

Dear Yujing,

Thank you very much for your help, but I still have a problem. I copied the 
files to create another SUBJECTS_DIR inside my Linux...I get the following 
error when I run the recon-all -all -s command:

gcm@LAP-LKP:~$ recon-all -all -s NowakG
fs-check-version --s NowakG --o /tmp/tmp.W9nDpk Sat Mar  2 19:14:18 CET 2024

setenv SUBJECTS_DIR /subjects
cd /home/gcm
/usr/local/freesurfer/7.3.2/bin/fs-check-version --s NowakG --o /tmp/tmp.W9nDpk 
-rwxr-xr-x 1 root root 18565 Aug  4  2022 
/usr/local/freesurfer/7.3.2/bin/fs-check-version

freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
$Id$
Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5
21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux pid 2145 Current FS Version
freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
bstampfile exists /subjects/NowakG/scripts/build-stamp.txt
Subject FS Version: 
freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% 
fs-check-version match = 1 fs-check-version Done
INFO: SUBJECTS_DIR is /subjects
Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2
-rw-rw-r-- 1 gcm gcm 89354 Mar  2 18:42 /subjects/NowakG/scripts/recon-all.log
Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5
21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
#
#@# MotionCor Sat Mar  2 19:14:18 CET 2024
ERROR: no run data found in /subjects/NowakG/mri. Make sure to have a volume 
called 001.mgz in  /subjects/NowakG/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: 
http://secure-web.cisco.com/1tuieePwmpGJNz-se1po4eAte-Piv-L3dyFVwTAhmaZp1yuYYA6WDplZIn_eOMWSQ6XNWLWosRbbqgelF1dP6cwLzm49NGnC06aPYcm9dVEqiJHPlKBBJdCOCc5UpBZKFISeT2vAsKPmtPe5bSN1PtnI37qzrEzfKZy04iVyZ7gO9j5K9chOEjC-f8PIW5LZ1QreMBW2MF4XAAmUD9cfwmgL-W-Xp87kV3_MnP7BzXmeq7Jcd1g7syzCCfGmQTOgp8StEekKQqnO96-4yhVqPeMcxevRvfvieGQEmdvybuW2fdVKNNP-v_6GslOFvUscl9fCLKOFTtLXKsa3Hnw_gYg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FConversion
Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5
21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s NowakG exited with ERRORS at Sat Mar  2 19:14:18 CET 2024

For more details, see the log file
/subjects/NowakG/scripts/recon-all.log
To report a problem, see
http://secure-web.cisco.com/1ufOUDYmRZBZH5OvNEdAvUSqehiGigkQXoMoJ5I3aSHOfsc36kcTvYNgNB3aBZ4jVdHB0nuAnVNJWxdRwzvXmwEPI3gDUdU4QRXnZbUR1wcB5OQxntw7Z5gopDmzqs9na5EBTZln5BzgpoULJxgLdPUVbjXFh90-tX1tjhSxELnft_ckbwlGbLrRKwrBBCKMy_wZKQlYHCq_mwPmJG9BFcPayLVp7kVjiKDvmTBGdY6Zu5EuMOFDJ2P8ZQVDTueZfXLtA67Bvr353l_R5YXyreMeaC-ozgMEC92WM24o5BpFOk4M0MsW9VOofqZy5uFd7nnpikbOdTUnpE4XwkWOz8A/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Could you please give me advice what is wrong?

Best regards,
Joanna



W dniu 2024-01-08 23:25, fsbuild napisał(a):
> External Email - Use Caution
> 
>   Let me add that it will not work to use shared mount point from the 
> Windows filesystem as you list below,
> 
>> /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri
> 
> - for your SUBJECTS_DIR when running a recon-all command.  The command 
> will fail because the Windows file system does not support soft-links.
>   Any SUBJECTS_DIR used for recon-all needs to be inside the Linux OS 
> image running freesurfer.  You could however copy the files from that 
> mount point to create another SUBJECTS_DIR somewhere inside your Linux 
> image, e.g., under your home directory in linux.
> 
> ... in your linux terminal window ...
> 
> $ cd
> $ mkdir subjects
> $ export SUBJECTS_DIR=$HOME/subjects
> $ cd $SUBJECTS_DIR
> $ cp -p -f -R /mnt/c/Users/GCM/Desktop/subjects/NowakG .
> 
> - R.
> 
> On Jan 8, 2024, at 16:10, Huang, Yujing 
> wrote:
> You need to specify the input files to process. Here is the wiki page 
> for recon-all -  
> https://secure-web.cisco.com/1BjMQpgiIYbM2liRLcu1lhuxV-DQbuX4Z-UYpPPpt
> MAbFi-NJiLZF1zFn86PASJOkrN6-GWw1d4D3OrHd1v-GqrcqNMoqsq_voJWaLftiEd-vak
> jsu5IvQ6kyUg5k7ghDpdCZU14EMBNDP8eYcsCjl1E5D5gNql2i-Y9Zu1Kpc6TuQh3odI2O
> ietrxyv5hM2H9YDVJ2J51cEZLa2CHRqUpe5QTE89g3k1kNK7jl8nNBK5kqYLoLEuZ-gJrr
> h_Ac2wDqYS5bIbjvKJN4lXnWjHzt6IJAq6spPNw_wAGm40hlLBAz-b5P1MtR3NajhBpUlp
> PBt-Yo9PLR0TwzBHrCLiHA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswi
> ki%2Frecon-all
> 
> Best,
> 
> Yujin

Re: [Freesurfer] Assistance Request: Issue with Merging .mgh Files in Ubuntu18

[Huang, Yujing]

Hi Rosie,

Are you trying to combine all volume files (.nii.gz) into one single volume by 
stacking all frames? Maybe you should use Freesurfer mri_concat instead of 
mrcalc?

Here are the help pages for mri_concat and mri_vol2surf:

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_concat
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf


Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rosie
Sent: Thursday, February 29, 2024 10:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Assistance Request: Issue with Merging .mgh Files in 
Ubuntu18


External Email - Use Caution
Dear Support Team,

I'm reaching out for assistance with merging two .mgh files.

As I try to generate a surface mapping for all subjects, I merged all volume 
files (.nii.gz) by mrcalc. So I get a volume file whose voxel value represents 
the number of valid subjects. And then I convert it to .mgh using mri_vol2surf. 
But the value of each voxel seems to be thrown out. Because I found the max 
value of .mgh is not the same as .nii file.

I guess I should merge files of all subject in mgh format to maintain the 
number of valid subjects, but it seems to be a volume encoded surface file 
format. So I don't know how to merge them.

I'm working on Ubuntu18.

I would be very grateful for your assistance.

Best,
Rosie




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Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

[Huang, Yujing]

All these filenames are too similar. You mentioned at least 3 different files.

mris_info 
fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii (error)
mris_info 
fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii(ok)
mris_convert 
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii (error)
ls -lt   
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii  (ok)

Make sure the file exists and provide full path to mris_info/mris_convert 
command.

If you continue to have problems with mris_info/mris_convert, share the .gii 
and we will take a closer look.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 4:41 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?


External Email - Use Caution

Hi again this gives


ls -lt fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
-rw-rw-r-- 1 karin karin 4323015 feb 29 21:54 
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
best

karin


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, February 29, 2024 10:29:25 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

It seems to me that it failed to open the .gii file.

Can you check if 
'fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii' exists and you 
have the read permission?
'ls -lt fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii'



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 4:09 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?


External Email - Use Caution

Hi I realized that the error occurs only with the Lh- file, that also gives 
this error


mris_info fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
** failed to open GIFTI XML file 
'fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii'
gifti_read_image() returned NULL

Is this a freesurfer error or is there something with the file?



thanks

Karin


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, February 29, 2024 10:05:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

The output from mris_info looks fine.

Are you still having trouble creating .annot file from a label.gii file? The 
command looks like this:

mris_convert --annot label/rh.aparc.annot.gii surf/rh.white.gii rh.aparc.annot

You need to provide full path to your input files.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 2:40 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?


External Email - Use Caution

Hi



Thank you for your reply! mri_info
 mris_info fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii
returns the follwoing:


==
gifti_image struct
version= 1
numDA  = 2
gim->meta nvpairs struct, len = 4 :
nvpair: 'Caret-Version' = '5.65'
nvpair: 'Date' = '2013-03-25T14:06:59'
nvpair: 'UniqueID' = '{ca14b266-2bf9-4910-8f46-7faecc9e1946}'
nvpair: 'encoding' = 'XML'

gim->labeltable giiLabelTable struct, len = 1 :
key 0, rgba (1.000, 1.000, 1.000, 0.000), label '???'

--
gim->darray[0] giiDataArray struct
intent   1008 = NIFTI_INTENT_POINTSET
datatype   16 = NIFTI_TYPE_FLOAT32
ind_ord 1 = RowMajorOrder
num_dim   = 2
dims  = 163842, 3, 0, 0, 0, 0
encoding3 = GZipBase64Binary
endian  2 = LittleEndian
ext_fname =
ext_offset= 0
darray->meta nvpairs struct, len = 9 :
nvpair: 'AnatomicalStructurePrimary' = 'CortexRight'
nvpair: 'AnatomicalStructureSecondary' 

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

[Huang, Yujing]

It seems to me that it failed to open the .gii file.

Can you check if 
'fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii' exists and you 
have the read permission?
'ls -lt fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii'



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 4:09 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?


External Email - Use Caution

Hi I realized that the error occurs only with the Lh- file, that also gives 
this error


mris_info fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
** failed to open GIFTI XML file 
'fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii'
gifti_read_image() returned NULL

Is this a freesurfer error or is there something with the file?



thanks

Karin


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, February 29, 2024 10:05:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

The output from mris_info looks fine.

Are you still having trouble creating .annot file from a label.gii file? The 
command looks like this:

mris_convert --annot label/rh.aparc.annot.gii surf/rh.white.gii rh.aparc.annot

You need to provide full path to your input files.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 2:40 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?


External Email - Use Caution

Hi



Thank you for your reply! mri_info
 mris_info fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii
returns the follwoing:


==
gifti_image struct
version= 1
numDA  = 2
gim->meta nvpairs struct, len = 4 :
nvpair: 'Caret-Version' = '5.65'
nvpair: 'Date' = '2013-03-25T14:06:59'
nvpair: 'UniqueID' = '{ca14b266-2bf9-4910-8f46-7faecc9e1946}'
nvpair: 'encoding' = 'XML'

gim->labeltable giiLabelTable struct, len = 1 :
key 0, rgba (1.000, 1.000, 1.000, 0.000), label '???'

--
gim->darray[0] giiDataArray struct
intent   1008 = NIFTI_INTENT_POINTSET
datatype   16 = NIFTI_TYPE_FLOAT32
ind_ord 1 = RowMajorOrder
num_dim   = 2
dims  = 163842, 3, 0, 0, 0, 0
encoding3 = GZipBase64Binary
endian  2 = LittleEndian
ext_fname =
ext_offset= 0
darray->meta nvpairs struct, len = 9 :
nvpair: 'AnatomicalStructurePrimary' = 'CortexRight'
nvpair: 'AnatomicalStructureSecondary' = 'MidLayer'
nvpair: 'Caret-Version' = '5.64'
nvpair: 'Date' = '2011-12-15T15:06:35'
nvpair: 'GeometricType' = 'Spherical'
nvpair: 'UniqueID' = '{1adeebae-d730-4e6c-8e93-b14805a6139f}'
nvpair: 'comment' = 'Imported from rh.sphere
scaled to fsaverage.rh.Midthickness_mni.mws.164k_fs.coord
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map'
nvpair: 'configuration_id' = 'Unknown'
nvpair: 'topo_file' = 'fsaverage.R.closed.164k_fs_R.topo'

darray->coordsys giiCoordSystem struct
dataspace  = NIFTI_XFORM_TALAIRACH
xformspace = NIFTI_XFORM_TALAIRACH
xform[0] :  1.00  0.00  0.00  0.00
xform[1] :  0.00  1.00  0.00  0.00
xform[2] :  0.00  0.00  1.00  0.00
xform[3] :  0.00  0.00  0.00  1.00
data   = 
nvals  = 491526
nbyper = 4
numCS  = 1
darray->ex_atrs nvpairs struct, len = 0 :
--
--
gim->darray[1] giiDataArray struct
intent   1009 = NIFTI_INTENT_TRIANGLE
datatype8 = NIFTI_TYPE_INT32
ind_ord 1 = RowMajorOrder
num_dim   = 2
dims  = 327680, 3, 0, 0, 0, 0
encoding3 = GZipBase64

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

[Huang, Yujing]

It looks like if you don't specify a subject (--target subject) as common 
space, it will default to 'fsaverage'.  See 
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc

The input to -surfreg <> is the surface registration to the common space. I 
think it should be a surface file not in .mgh format.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Asuka Toyofuku
Sent: Wednesday, February 28, 2024 8:07 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Creating a custom registration template with 
FreeSurfer template


External Email - Use Caution
Hi, thanks for your suggestion.

I added .mgh at the end of the input and output file, but I got a different 
type of error.

for d in Teen*
> do mris_preproc --surfreg sphere.reg.teenheart_average_template.mgh --s $d 
> --hemi lh --out lh.surfreg.teenheart_average_template.thickness.mgh --meas 
> thickness
> done
ERROR: cannot find fsaverage in /media/m-ssd5/FS7_Teen
ERROR: cannot find fsaverage in /media/m-ssd5/FS7_Teen
ERROR: cannot find fsaverage in /media/m-ssd5/FS7_Teen
...

Do we need the fsaverage folder when creating a custom template?
There is for example, lh.fsaverage.sphere.reg file in addition to 
sphere.reg.teenheart_average_template.

The previous error was ; ERORR: format for 
lh.surfreg.teenheart_average_template.thickness not recognized.
This time, the problem seems to lie in not having fsaverage folder, rather than 
the format for the thickness template?

Any input is appreciated.

Best,
Asuka

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>
Sent: 26 February 2024 18:22
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Creating a custom registration template with 
FreeSurfer template

You need to specify a format for the output (eg, ...thickness.mgz)
On 2/26/2024 10:31 AM, Asuka Toyofuku wrote:

External Email - Use Caution
Hi, many thanks for your reply.
Here's the terminal output;

asuka@rigi:/media/.../FS7_Teen$ for d 
in Teen* EPK* epk*
> do mris_preproc --surfreg sphere.reg.teenheart_average_template --s $d --hemi 
> lh --out lh.surfreg.teenheart_average_template.thickness --meas thickness
> done
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized

Error continued so I stopped running at a certain point.
What do you think?

Best regards,
Asuka

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: 23 February 2024 19:30
To: freesurfer@nmr.mgh.harvard.edu 

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

Can you include the full terminal output for one of the mris_preproc commands 
that is failing?
On 2/22/2024 7:12 AM, Asuka Toyofuku wrote:
External Email - Use Caution

Dear Freesurfer experts,



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



According to the instructions, we need to

1) Create an average subject (Creat

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

[Huang, Yujing]

The output from mris_info looks fine.

Are you still having trouble creating .annot file from a label.gii file? The 
command looks like this:

mris_convert --annot label/rh.aparc.annot.gii surf/rh.white.gii rh.aparc.annot

You need to provide full path to your input files.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 2:40 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?


External Email - Use Caution

Hi



Thank you for your reply! mri_info
 mris_info fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii
returns the follwoing:


==
gifti_image struct
version= 1
numDA  = 2
gim->meta nvpairs struct, len = 4 :
nvpair: 'Caret-Version' = '5.65'
nvpair: 'Date' = '2013-03-25T14:06:59'
nvpair: 'UniqueID' = '{ca14b266-2bf9-4910-8f46-7faecc9e1946}'
nvpair: 'encoding' = 'XML'

gim->labeltable giiLabelTable struct, len = 1 :
key 0, rgba (1.000, 1.000, 1.000, 0.000), label '???'

--
gim->darray[0] giiDataArray struct
intent   1008 = NIFTI_INTENT_POINTSET
datatype   16 = NIFTI_TYPE_FLOAT32
ind_ord 1 = RowMajorOrder
num_dim   = 2
dims  = 163842, 3, 0, 0, 0, 0
encoding3 = GZipBase64Binary
endian  2 = LittleEndian
ext_fname =
ext_offset= 0
darray->meta nvpairs struct, len = 9 :
nvpair: 'AnatomicalStructurePrimary' = 'CortexRight'
nvpair: 'AnatomicalStructureSecondary' = 'MidLayer'
nvpair: 'Caret-Version' = '5.64'
nvpair: 'Date' = '2011-12-15T15:06:35'
nvpair: 'GeometricType' = 'Spherical'
nvpair: 'UniqueID' = '{1adeebae-d730-4e6c-8e93-b14805a6139f}'
nvpair: 'comment' = 'Imported from rh.sphere
scaled to fsaverage.rh.Midthickness_mni.mws.164k_fs.coord
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map'
nvpair: 'configuration_id' = 'Unknown'
nvpair: 'topo_file' = 'fsaverage.R.closed.164k_fs_R.topo'

darray->coordsys giiCoordSystem struct
dataspace  = NIFTI_XFORM_TALAIRACH
xformspace = NIFTI_XFORM_TALAIRACH
xform[0] :  1.00  0.00  0.00  0.00
xform[1] :  0.00  1.00  0.00  0.00
xform[2] :  0.00  0.00  1.00  0.00
xform[3] :  0.00  0.00  0.00  1.00
data   = 
nvals  = 491526
nbyper = 4
numCS  = 1
darray->ex_atrs nvpairs struct, len = 0 :
--
--
gim->darray[1] giiDataArray struct
intent   1009 = NIFTI_INTENT_TRIANGLE
datatype8 = NIFTI_TYPE_INT32
ind_ord 1 = RowMajorOrder
num_dim   = 2
dims  = 327680, 3, 0, 0, 0, 0
encoding3 = GZipBase64Binary
endian  2 = LittleEndian
ext_fname =
ext_offset= 0
darray->meta nvpairs struct, len = 5 :
nvpair: 'Caret-Version' = '5.616'
nvpair: 'Date' = '2011-01-24T21:13:13'
nvpair: 'TopologicalType' = 'Closed'
nvpair: 'UniqueID' = '{15ec5dcb-b08c-420e-a8f9-057cbd2c0706}'
nvpair: 'comment' = 'Imported from rh.sphere'

data   = 
nvals  = 983040
nbyper = 4
numCS  = 0
darray->ex_atrs nvpairs struct, len = 0 :
--
gifti_image struct
swapped= 0
compressed = 1
 -- darray totals: 6 MB
gim->ex_atrs nvpairs struct, len = 2 :
nvpair: 'xmlns:xsi' = 'true'
nvpair: 'xsi:noNamespaceSchemaLocation' = 'true'

==
Best

Karin


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Monday, February 26, 2024 4:21:01 PM
To: Freesurfer support list
Subject: [ext] Re: [Freesurfer] mris_convert reading surf.gii files?

Your mris_convert command looks correct. I'm able to do the conversion like 
this with dev version:

mris_convert --annot

Re: [Freesurfer] mris_convert reading surf.gii files?

[Huang, Yujing]

Your mris_convert command looks correct. I'm able to do the conversion like 
this with dev version:

mris_convert --annot label/rh.aparc.annot.gii surf/rh.white.gii rh.aparc.annot

I'm wondering which Freesurfer you are running. If you do 'mris_info surf.gii', 
what does it report?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Westin, Karin
Sent: Saturday, February 24, 2024 6:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_convert reading surf.gii files?


External Email - Use Caution

Hi



I'm trying to create an .annot file from a label.gii file using an HCP 
fsavarage.surf.gii file (eg mris_convert --annot my_label.label.gii 
fsaverage_template.L.surf.gii lh.my_annot.annot). However I keep getting the 
error



** failed to open GIFTI XML file 
'fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii'

mrisReadGIFTIdanum: gifti_read_image() returned NULL

Is there a better way to read/open CIFTI files using mris_convert?

Best and thanks
Karin

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

[Huang, Yujing]

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

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

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

Thanks,
Mitch

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

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

Hi FS Devs,



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



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

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



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



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



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



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

Best,
Mitch



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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 
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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. 

Re: [Freesurfer] Grey Matter Intensities

[Huang, Yujing]

How about this command:

mri_segstats --seg $FREESURFER_HOME/subjects/bert/mri/aparc+aseg.mgz --i 
$FREESURFER_HOME/subjects/bert/mri/orig.mgz --sum bert-orig.aparc+aseg.sum

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ERNEST KISSI
Sent: Wednesday, February 21, 2024 12:52 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Grey Matter Intensities


External Email - Use Caution
There is no such flag in mri_segstats to calculate gray matter cortical 
parcels. There is a flag for total gray matter rather. Nevertheless, I think 
there is a file in recon-all output that has white matter to gray matter ratio 
: lh.w-g.pct and rh.w-g.pct and I have a file for the white matter so I think I 
may be able to create a code to calculate the gray matter.

On Wed, Feb 21, 2024 at 7:21 PM Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>> wrote:
I think that is exactly one of the outputs of mri_segstats. Check the help on 
it and see if it does what you want. I believe it is also run by default during 
recon-all and the values placed into one of the stats output files

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of ERNEST KISSI
Sent: Wednesday, February 21, 2024 11:14 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Grey Matter Intensities


External Email - Use Caution
Yes, please
That's exactly what I mean.

On Wed, Feb 21, 2024, 6:44 PM Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>> wrote:
Can you clarify what you mean by “measure the intensities for the grey matter 
regions”? You could for example compute the mean gray matter intensity within 
each cortical parcel and each subcortical structure. Is that what you want?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of ERNEST KISSI
Sent: Wednesday, February 21, 2024 9:45 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Grey Matter Intensities


External Email - Use Caution
I think these are not grey matter but cortical parcellation.
FSL can output grey matter segmentation but I do not think freesurfer has such 
an output.
In aparc.stats (rh.aparc or lh.aparc), there is only GrayVol and no intensity 
measure. I want to know how I can measure the intensities for the grey matter 
regions.

On Wed, Feb 21, 2024, 5:25 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
Recon-all outputs these 3 aparc aseg volumes:

aparc.DKTatlas+aseg.mgz
aparc.a2009s+aseg.mgz
aparc+aseg.mgz


Are these what you are looking for? They should work the same way as aseg 
volume.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of ERNEST KISSI
Sent: Tuesday, February 20, 2024 3:22 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Grey Matter Intensities


External Email - Use Caution
Hi Freesurfer team,

Recon-all output  shows the white matter volumes and white matter  intensities 
of different brain regions but only shows grey matter volumes. I want to know 
if there is a function or a flag to also get information on the regional grey 
matter intensities.

Thank you.
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Re: [Freesurfer] Grey Matter Intensities

[Huang, Yujing]

Recon-all outputs these 3 aparc aseg volumes:

aparc.DKTatlas+aseg.mgz
aparc.a2009s+aseg.mgz
aparc+aseg.mgz


Are these what you are looking for? They should work the same way as aseg 
volume.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ERNEST KISSI
Sent: Tuesday, February 20, 2024 3:22 PM
To: Freesurfer support list 
Subject: [Freesurfer] Grey Matter Intensities


External Email - Use Caution
Hi Freesurfer team,

Recon-all output  shows the white matter volumes and white matter  intensities 
of different brain regions but only shows grey matter volumes. I want to know 
if there is a function or a flag to also get information on the regional grey 
matter intensities.

Thank you.
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Re: [Freesurfer] Errors with Recon-all

[Huang, Yujing]

There is an error before the 'multiple frames error':
"
Found 384 DICOM file(s)
load Image 
/Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855821.dcm,
 size 114688
Warning: Unable to determine slice direction: please check whether slices are 
flipped
Warning: Unable to determine slice direction: please check whether slices are 
flipped
Convert 384 DICOM (224x256x192x2)
DICOM row order preserved: may appear upside down in tools that ignore spatial 
transforms
WARNING: MRIsetRas2VoxFromMatrix(): voxels sizes are inconsistent
   (0.976562,0.976562) (0.976562,0.976562) (1,0)
This is probably due to shear in the vox2ras matrix
Input Vox2RAS --
-0.97656   0.0  -0.0   105.30721;
-0.0  -0.97656  -0.0   122.96610;
0.0   0.0   0.0  -113.12712;
0.0   0.0   0.0   0.0;
TR=2000.00, TE=3.03, TI=1100.00, flip angle=15.00
i_ras = (-1, -4.897e-12, 0)
j_ras = (4.897e-12, -1, 0)
k_ras = (nan, nan, nan)
"

Let's see if we can have it resolved first. Freesurfer internally uses dcm2niix 
to convert dicoms. Can you try Freesurfer dev version to see if latest dcm2niix 
fix the error?

Also, I noticed your SUBJECTS_DIR points to your FS install directory. It is a 
good idea to point it to some other directory where you have write permission.
"
INFO: SUBJECTS_DIR is /Applications/freesurfer/7.4.1/subjects
Actual FREESURFER_HOME /Applications/freesurfer/7.4.1
"

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Perumalla, Sucika
Sent: Tuesday, February 20, 2024 3:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Errors with Recon-all

Dear Freesurfer Support Services,

My name is Sucika Perumalla and I get the multiple frames errors when trying to 
run recon-all with my dicoms even after extracting the multiple frames. I was 
wondering if you can please help resolve these issues.

Thanks
_
Sucika Perumalla
Clinical Research Assistant I
Department of Neurology, Division of Movement Disorders
Brigham and Women's Hospital
60 Fenwood Road, Boston, MA 02115
sperumal...@bwh.harvard.edu | 508-414-2601

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Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

[Huang, Yujing]

I see the problem.

In ‘usage_exit:’ section, you will notice several echo statements are split 
into two lines. Fix those lines and try again. ‘“tcsh -x 
$FREESURFER_HOME/bin/mri_glmfit-sim –help” will help you identify those lines.

Best,

Yujing

From: Sven Kühn 
Sent: Saturday, February 10, 2024 5:09 AM
To: Freesurfer support list ; Huang, Yujing 

Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat


External Email - Use Caution

Many thanks for the answer! Sorry, there seems to be some context missing. I 
was replying to an old post from the archives and thought it would attach 
itself there. I copied the script for mri_glmfit-sim from that post.
Here is the link to it:

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg68973.html<https://secure-web.cisco.com/1C0tWp9a2AtgW6pz_K_YQQcl2gRLBm9YoGcFQf6OVnEWfU4xw_g9pNGtHahFmsjDHViYZcmLpx46sC-hnSXa_-HO_SWPh8Rn69JL37CIR4BjCC2U3i4xsmKBMaXA4_fmUDv9NRW_O_bKJKzfaVrQC37KFNK6gZM67pA5BkW2Ex3X4Q5zL3-hcBKuwPldhBY6uZ4u0mS_5yi_DNx3l0Te4GrqRDFTtFiqWBLEESSTbjtSiQQqKooQRy9pyYoJ61tWb3JVMXq7WAbovDlQzXcpt-kYgTcG3RPZ3ywYqskFJEZhEebype-G7ouR1yX1s4lLa/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg68973.html>

I think the mistake is that I didn't convert it into a script properly. Could 
you perhaps provide me with the script as a file? I would like to get the 
volume of each subject from the ocn.dat by adding --spatial-sum to the command 
line. Exactly as described in the post.

Best

Sven




Am 06.02.24 um 15:16 schrieb Huang, Yujing:
I can’t reproduce the error here with FS 6.0. Not sure where you downloaded the 
script. Can you run this “tcsh -x $FREESURFER_HOME/bin/mri_glmfit-sim –help”? 
I’m hoping it will give some hints.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 On Behalf Of Sven Kühn
Sent: Sunday, February 4, 2024 12:09 PM
To: Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>; 
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat


External Email - Use Caution

Hi Dr. Greve, hi all

I have tried your code. I copied it from the website into a text file and 
replaced mri_glmfit-sim in the freesurfer/bin folder. The file is executable 
but aborts after a few lines with no indication of a cause. The following 
output is generated:



xx@xxx:~/Schreibtisch/WMH_DCS$ mri_glmfit-sim --glmdir rh.volume.DCS.10.glmdir 
--cache 2.3 abs --cwp 0.05 --2spaces --spatial-sum
cmdline mri_glmfit.bin --y rh.volume.DCS.10.mgh --fsgd FSGD/DCSstudy.fsgd --C 
Contrasts/DCS-DCSK.mtx --C Contrasts/DCSK-DCS.mtx --surf fsaverage rh --cortex 
--glmdir rh.volume.DCS.10.glmdir
SURFACE: fsaverage rh
Unmatched `.

Even if I run --help, only some of the lines appear:

mri_glmfit-sim --help

 --glmdir glmdir
 --cwp cwthresh : cluster-wise p-value threshold (.05)

Use pre-computed z-based monte-carlo simulations (see mri_mcsim)
 --mczsim vwthreshold sign
If you have run your own simulations (mri_mcsim), then specify
   --mczsim-dir dir : default is FREESURFER_HOME/average/mult-comp-cor
   --mczsim-label label : default is cortex

Use permutation simulation
 --perm nsim CFT sign : permutation simulation with nsim iterations
Unmatched ".

Do you have any idea why this might be?
Like Xiaoxu before me, I have already tried to convert the file with dos2unix. 
However, without the desired effect.

I am using Linux Ubuntu 16.04 and Freesurfer Vers. 6.0.

I would be very grateful for any tips.

Best regards



sven



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

[Huang, Yujing]

Hi Stefano,

I looked at the log files that you sent in a separate email. I see 2 problems 
here:
1. when running preproc-sess with -nomc option,  rawfunc2surf-sess couldn't 
find file fmcpr.up or fmcpr.even in the directory
2. I think the 'if: Expression Syntax' error is from stem2fname

To confirm #2, can you try 'stem2fname 
/home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/brainmask'
 from your command line?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stefano Delli Pizzi
Sent: Tuesday, February 13, 2024 4:32 AM
To: Greve, Douglas N.,Ph.D. ; Freesurfer support list 

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


External Email - Use Caution
Thank you.
Stefano


Binarizing based on threshold
min1e-09
max+infinity
binval1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 149926 values in range
Counting number of voxels in first frame
Found 149925 voxels in final mask
Writing output to 
/Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/masks/brain.fsaverage.rh.pr.nii.gz
Count: 149925 149925.00 163842 91.505841
mri_binarize done
  1/1 003_S_6014 001 lh -
Mar 13 Feb 2024 10:28:12 CET
ERROR: could not determine file for 
/Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/fmcpr.even
if ( $status ) exit 1 ;
if ( 1 ) exit 1
exit 1
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Re: [Freesurfer] Problem with mris_remiesh in recon-all

[Huang, Yujing]

I'm not familiar with the logic. The program is calling 
Remesher::removeCollapsedTrias() from remesher.cpp in loops. The program will 
get out of loop when Remesher::removeCollapsedTrias() returns -1.

I can take a closer look if I have access to the data.

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Iglesias Gonzalez, Juan E.
Sent: Monday, February 12, 2024 3:46 PM
To: Freesurfer support list 
Cc: Bocchetta, Martina 
Subject: [Freesurfer] Problem with mris_remiesh in recon-all

Dear experts,
My collaborator Martina Bocchetta is encountering a weird problem with 
recon-all, specifically with mris_remesh after the topology correction (see 
below).
Any insight?
Thanks in advance,
/Eugenio


mris_remesh --remesh --iters 3 --input /path/to/subject/surf/rh.orig.premesh 
--output /path/to/subjects/surf/rh.orig

iters = 3
standard remeshing without target
   adjusted l: 0.707317
remeshing to edge length 0.707317 with 3 iterations
Remesher::removeCollapsedTrias( 132651 , 132650 )
v_to_t[vidx] : [265322, 265325, ]
Trias are identical : ... removing ...
Remesher::removeTria( 265325 )
e_to_t[ 661301 ] before: [265322, 265325, ]
e_to_t[ 661301 ] after: [265322, ]
e_to_t[ 134659 ] before: [265325, 265322, ]
e_to_t[ 134659 ] after: [265322, ]
e_to_t[ 661307 ] before: [265325, 265322, ]
e_to_t[ 661307 ] after: [265322, ]
Remesher::removeTria( 265322 )
e_to_t[ 661301 ] before: [265322, ]
e_to_t[ 661301 ] after:
 e_to_t[ 661307 ] before: [265322, ]
e_to_t[ 661307 ] after:
 e_to_t[ 134659 ] before: [265322, ]
e_to_t[ 134659 ] after:
 NEXTIDX : 132658
Remesher::removeCollapsedTrias( 132658 , 132650 )
v_to_t[vidx] :
 Trias are identical : ... removing ...
Remesher::removeTria( 265325 )
Remesher::removeTria( 265322 )
NEXTIDX : 132651

... and you fall in an infinite loop with messages like these printed over and 
over.


--
Juan Eugenio Iglesias
http://www.jeiglesias.com
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Re: [Freesurfer] Calculation of MRI intensity

[Huang, Yujing]

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

Best,

Yujing


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


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

[Huang, Yujing]

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

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

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

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

Best,

Yujing


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


External Email - Use Caution

Dear Freesurfer experts,



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


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


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


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

Best regards,
Asuka
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Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

[Huang, Yujing]

I can’t reproduce the error here with FS 6.0. Not sure where you downloaded the 
script. Can you run this “tcsh -x $FREESURFER_HOME/bin/mri_glmfit-sim –help”? 
I’m hoping it will give some hints.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Sven Kühn
Sent: Sunday, February 4, 2024 12:09 PM
To: Greve, Douglas N.,Ph.D. ; 
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat


External Email - Use Caution

Hi Dr. Greve, hi all

I have tried your code. I copied it from the website into a text file and 
replaced mri_glmfit-sim in the freesurfer/bin folder. The file is executable 
but aborts after a few lines with no indication of a cause. The following 
output is generated:



xx@xxx:~/Schreibtisch/WMH_DCS$ mri_glmfit-sim --glmdir rh.volume.DCS.10.glmdir 
--cache 2.3 abs --cwp 0.05 --2spaces --spatial-sum
cmdline mri_glmfit.bin --y rh.volume.DCS.10.mgh --fsgd FSGD/DCSstudy.fsgd --C 
Contrasts/DCS-DCSK.mtx --C Contrasts/DCSK-DCS.mtx --surf fsaverage rh --cortex 
--glmdir rh.volume.DCS.10.glmdir
SURFACE: fsaverage rh
Unmatched `.

Even if I run --help, only some of the lines appear:

mri_glmfit-sim --help

 --glmdir glmdir
 --cwp cwthresh : cluster-wise p-value threshold (.05)

Use pre-computed z-based monte-carlo simulations (see mri_mcsim)
 --mczsim vwthreshold sign
If you have run your own simulations (mri_mcsim), then specify
   --mczsim-dir dir : default is FREESURFER_HOME/average/mult-comp-cor
   --mczsim-label label : default is cortex

Use permutation simulation
 --perm nsim CFT sign : permutation simulation with nsim iterations
Unmatched ".

Do you have any idea why this might be?
Like Xiaoxu before me, I have already tried to convert the file with dos2unix. 
However, without the desired effect.

I am using Linux Ubuntu 16.04 and Freesurfer Vers. 6.0.

I would be very grateful for any tips.

Best regards



sven
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Re: [Freesurfer] if: Expression Syntax - preproc-sess

[Huang, Yujing]

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

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stefano Delli Pizzi
Sent: Saturday, February 3, 2024 2:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] if: Expression Syntax - preproc-sess


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to run preproc-sess with -nomc option



preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest

-per-run -sliceorder up -force

if: Expression Syntax.



This error occurred before to create the file with slice timing correction



The error did not occur when I run the preproc-sess command line without the

-nomc option.



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

have any thoughts on how to trouble-shoot this one?



FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460

Platform: Darwin Kernel Version 21.6.0
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Re: [Freesurfer] ERROR: mri_ca_register with non-zero status 9

[Huang, Yujing]

It looks like your recon-all was killed. Is it possible that your recon-all ran 
out of the job limit (time, memory, ...).

I also noticed you have these options to recon-all '-3T -no-isrunning'. Make 
sure you don't have other instance of recon-all running on the same subject.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Lucas Alexis Ronat
Sent: Tuesday, February 6, 2024 12:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ERROR: mri_ca_register with non-zero status 9


External Email - Use Caution
Hello FreeSurfer developers,

I'm trying to process structural MRI (T1w.nii) using the recon-all command but 
I get the following error:
ERROR: mri_ca_register with non-zero status 9

Similar errors have been reported but I am unable to resolve this problem. Do 
you have any details on how to fix this? I have also attached the latest 
recon-all.log file in case it is useful.

1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460
2) Platform: Alliance Canada Graham cluster (via MobaXterm terminal)
3) uname -a : Linux gra-login2 3.10.0-1160.88.1.el7.x86_64 #1 SMP Tue Mar 7 
15:41:52 UTC 2023 x86_64 GNU/Linux
4) recon-all.log : see attached

I got a similar error on the Niagara cluster using FreeSurfer version 7.1.0 
(ERROR: mri_ca_register with non-zero status 24)

Thanks for your help

Lucas Ronat
Postdoctoral Fellow
Douglas Research Center, Montreal, Canada
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Re: [Freesurfer] Euler number calculation from number of holes

[Huang, Yujing]

Just checked mris_euler_number,  holes are calculated from euler number: holes 
= 1-eno/2


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, February 1, 2024 10:27 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Euler number calculation from number of holes

Hi Melissa

mris_euler_number 

writes out a bunch of stuff, including the Euler number:

mris_euler_number ~/links/subjects/bruce.dev/surf/lh.orig.nofix
euler # = v-e+f = 2g-2: 154526 - 463668 + 309112 = -30 --> 16 holes
  F =2V-4:  309112 != 309052-4 (-64)
  2E=3F:927336 = 927336 (0)

total defect index = 32

so -30 in this case. Is that what you wanted?

Cheers
Bruce
From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Melissa Thalhammer
Sent: Thursday, February 1, 2024 5:31 AM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Euler number calculation from number of holes


External Email - Use Caution

Dear FreeSurfer experts,



I want to calculate Euler numbers for QC but I am not sure how to get them. I 
read some posts here and figured out that I get the number of holes in a 
surface with mris_euler_number -o $OUTPUT_FILE $subject/surf/?h.orig.nofix. Is 
it correct that I need to calculate the Euler number subsequently as the sum of 
holes of both surfaces and then Euler_number=(number_of_holes*(-2)) -2 ?



Best, Melissa



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Re: [Freesurfer] converting preprecessed functional surface data to gifti

[Huang, Yujing]

The output looks correct to me.

The functional gifti file doesn't have the vertex coordinate information. It is 
like a surface overlay. It only contains one value for each vertex.

The pial and white surface gifti files have the vertex coordinates and 
information about how triangles are formed.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of wangzhiwei3233
Sent: Tuesday, January 30, 2024 1:27 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] converting preprecessed functional surface data to 
gifti


External Email - Use Caution

Dear Yujing,

Thank you for your response.

I attempted the command again as follows:

mris_convert -f $funcfile ${SUBJECTS_DIR}/fsaverage/surf/${hemi}.white 
./$fname.gii



This time, no errors were reported. However, upon comparison, it appears that 
the output gii file is identical (same file size) to the output from the 
following command line:

mri_convert $funcfile  ./$fname.gii (Note: mri_convert, not mris_convert)

The content of the output file is as follows:





http://gifti.projects.nitrc.org/gifti.dtd";>



   

  

 

 

  

  

 

 

  

  

 

 

  

   

   

   

  

  
eJysunV4ldfWtxsh7u7utuLua95xJ8RICQQnFA1OCQQIWjQ4xYsXdyheNDR4sKLBKSSEIkkg+Z69r+vd17fP6dnvOd975j9rZeVZz5xzzDF+4/(.more
 lines like this, not shown )



It appears that there is no vertex coordinate information in it. I am uncertain 
whether the output result file is correct. What should the output file look 
like?



My ultimate goal is to perform GLM analysis in SPM using these gii data. The 
'gifti' function in SPM can read the output gii file, but it contains only 
values (cdata: 163842×1 single), as I split the frames, so the frame is "×1". 
This leads to errors in further analysis. I also converted the pial surface to 
gii and read it using the 'gifti' function in SPM; it contained three fields:

 faces: [327680×3 int32]

 mat: [4×4 double]

vertices: [163842×3 single]

It seems that there is no problem with converting the pial surface to gii, but 
there is an issue with converting functional surface data to gii.



Best,

zhiwei



Date: Fri, 26 Jan 2024 13:29:24 +

From: "Huang, Yujing" 
mailto:yhuan...@mgh.harvard.edu>>

Subject: Re: [Freesurfer] converting preprecessed functional surface

   datatogifti

To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>

Message-ID:

 
mailto:mn2pr04mb5982358d1de7cf24b4127e7c9d...@mn2pr04mb5982.namprd04.prod.outlook.com>>



Content-Type: text/plain; charset="utf-8"



How does your command line look like?  To convert functional file, use ?-f 
?. You also need to specify surface file.



Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of wangzhiwei3233

Sent: Friday, January 26, 2024 4:39 AM

To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>

Subject: [Freesurfer] converting preprecessed functional surface data to gifti





External Email - Use Caution

Dear Freesurfer experts,

How can I convert the preprecessed  functional surface data to gifti 
format(gii)?

I tried mris_convert, but I encountered the following error.

error: freadFloat: fread failed



Your assistance  would be highly appreciated.



Best regards,

zhiwei
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Re: [Freesurfer] converting preprecessed functional surface data to gifti

[Huang, Yujing]

How does your command line look like?  To convert functional file, use ‘-f 
’. You also need to specify surface file.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of wangzhiwei3233
Sent: Friday, January 26, 2024 4:39 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] converting preprecessed functional surface data to gifti


External Email - Use Caution
Dear Freesurfer experts,
How can I convert the preprecessed  functional surface data to gifti 
format(gii)?
I tried mris_convert, but I encountered the following error.
error: freadFloat: fread failed

Your assistance  would be highly appreciated.

Best regards,
zhiwei
---
Zhiwei Wang（王志伟), Associate Investigator
International Center for Primate Brain Research
Center for Excellence in Brain and Intelligence Technology
Institute of Neuroscience,Chinese Academy of Sciences
Room 215, Building #5, 500 Qiangye Road, Shanghai, 201602,China

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Re: [Freesurfer] recon-all ends prematurely without error

[Huang, Yujing]

Your recon-all command doesn't have the directive to tell it what to run - add 
option '-all' to your command.

See this wiki page for detail 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Weisholtz, Daniel S.,MD
Sent: Thursday, January 25, 2024 12:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all ends prematurely without error

Hello FreeSurfer team,

I have been using FreeSurfer for some time without difficulty, but I recently 
encountered a problem that I cannot overcome.  When I run recon-all using a 
command like this:

recon-all -s b047test -i 
/Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz


the process terminates in just a few seconds without error.

The output reads as follows:
fs-check-version --s b047test --o 
/var/folders/44/ndjzqbx515991v_9vt0j8sprgq/T//tmp.IMS2K1
Thu Jan 25 12:35:02 EST 2024

setenv SUBJECTS_DIR /Users/danielweisholtz/Coregistration/subjects
cd /Users/danielweisholtz
/Applications/freesurfer/7.4.1/bin/fs-check-version --s b047test --o 
/var/folders/44/ndjzqbx515991v_9vt0j8sprgq/T//tmp.IMS2K1
-rwxr-xr-x  1 root  wheel  18565 Jun 14  2023 
/Applications/freesurfer/7.4.1/bin/fs-check-version

freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
$Id$
Darwin i.partners.org 21.6.0 Darwin Kernel Version 
21.6.0: Mon Aug 22 20:19:52 PDT 2022; 
root:xnu-8020.140.49~2/RELEASE_ARM64_T6000 arm64
pid 6977
Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
Subject does not have a bstampfile, copying 
/Applications/freesurfer/7.4.1/build-stamp.txt
Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
No constraints on version because REQ=UnSet and FsVerFile=NotThere
#@#% fs-check-version match = 1
fs-check-version Done
INFO: SUBJECTS_DIR is /Users/danielweisholtz/Coregistration/subjects
Actual FREESURFER_HOME /Applications/freesurfer/7.4.1
Darwin i.partners.org 21.6.0 Darwin Kernel Version 
21.6.0: Mon Aug 22 20:19:52 PDT 2022; 
root:xnu-8020.140.49~2/RELEASE_ARM64_T6000 arm64
/Users/danielweisholtz/Coregistration/subjects/b047test
\n mri_convert 
/Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz
 /Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz \n
mri_convert 
/Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz
 /Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz
INFO: using NIfTI-1 qform
reading from 
/Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz...
INFO: This is an unsigined short.
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (0, 0, 1)
writing to 
/Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz...
~/Coregistration/subjects/b047test/mri/transforms 
~/Coregistration/subjects/b047test
~/Coregistration/subjects/b047test

Started at Thu Jan 25 12:35:02 EST 2024
Ended   at Thu Jan 25 12:35:06 EST 2024
#@#%# recon-all-run-time-hours 0.001
recon-all -s b047test finished without error at Thu Jan 25 12:35:06 EST 2024
done



The subject folder is created along with some of the files, but not much is 
actually there. I had been using FreeSurfer 7.2.0 but I upgraded to 7.4.1, and 
this did not resolve the problem.  Initially, I thought the problem was with 
the source file I was using, but I tested it with an MRI that I had previously 
used successfully with recon-all, and I got the same error. So something seems 
to have changed with my system that is causing this problem.

I am running FreeSurfer on a Mac using MacOS 12.6.

Many thanks for any assistance you can provide.

Sincerely,
Dan Weisholtz


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Re: [Freesurfer] MRIread and RAS orientation

[Huang, Yujing]

Does fslorient resample the image to have the data on disk reoriented? If not, 
as Bruce and Eugenio commented, it is reading the same data with same 
orientation.

I think you can use ‘mri_diff --notallow-geo f1 f2’ to check if f1 and f2 have 
the same data orientation on disk.

You can use ‘mri_vol2vol --mov  --targ  --regheader --o 
 --interp nearest’ to reorient the data.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fotiadis, Panagiotis
Sent: Tuesday, January 23, 2024 12:11 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] MRIread and RAS orientation


External Email - Use Caution
Thanks, Bruce! Just to reiterate my previous message below, would you happen to 
know why the MRI.vol matrices of both files come out looking identical?

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

Thank you all again!

Best,
Panos

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>>
Date: Tuesday, January 23, 2024 at 11:06 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] MRIread and RAS orientation
I agree with Eugenio – it doesn’t do any resampling. Just reads in the data as 
is

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Tuesday, January 23, 2024 8:49 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] MRIread and RAS orientation

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

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

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Fotiadis, Panagiotis
Sent: Tuesday, January 23, 2024 1:54 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] MRIread and RAS orientation


External Email - Use Caution
Hello,

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

Thanks in advance!

Best,
Panos

**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues

**
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] File extension .area failures

[Huang, Yujing]

Not sure what kind of server you are running. Maybe your IT can help with the 
file extension issue.

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of James Bartolotti
Sent: Monday, January 22, 2024 6:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] File extension .area failures


External Email - Use Caution
The MR data on network drives at our institute were recently migrated to a new 
server. After the migration, recon-all in freesurfer fails to complete. The 
issue is that freesurfer generates files with the extension ".area", including 
lh.area and rh.area, but the .area extension is forbidden on the server and the 
files will not be created.

Has anyone ever had issues with an .area extension? Are there any possible 
workarounds to change the .area extension used by freesurfer?




James Bartolotti, Ph.D. (he/him/his)

Senior Scientist

Structure and Function Unit, Hoglund Biomedical Imaging Center

University of Kansas Medical Center

jbartolot...@kumc.edu
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Re: [Freesurfer] MRIread and RAS orientation

[Huang, Yujing]

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

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

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fotiadis, Panagiotis
Sent: Tuesday, January 23, 2024 1:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] MRIread and RAS orientation


External Email - Use Caution
Hello,

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

Thanks in advance!

Best,
Panos

**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues
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Re: [Freesurfer] recon-all cannot execute: required file not found

[Huang, Yujing]

I'm wondering how you ran recon-all.  Do you see the error even running it w/o 
any arguments?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:59 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found

Thanks Yujing,
Yes, I looked for the file permissions using ls -l. It does have execute 
permissions.
I also tried running chmod which didn't help.

Thanks,
Noam

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Friday, January 19, 2024 2:54 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found


After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.



1. 'ls -l $FREESURFER_HOME/bin/recon-all' to check if your recon-all has the 
execute permissions?

2. use 'chmod +x $FREESURFER_HOME/bin/recon-all' to grant the permission





Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all cannot execute: required file not found



Dear group,

I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)

I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)

After sourcing Freesurfer, recon-all gives following error:

.../freesurfer/bin/recon-all: cannot execute: required file not found



Other functions, e.g. freeview, mri_info, all seem to work as expected



Would love some help.

Thanks,

Noam




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Re: [Freesurfer] recon-all cannot execute: required file not found

[Huang, Yujing]

After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.

1. 'ls -l $FREESURFER_HOME/bin/recon-all' to check if your recon-all has the 
execute permissions?
2. use 'chmod +x $FREESURFER_HOME/bin/recon-all' to grant the permission


Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all cannot execute: required file not found

Dear group,
I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)
I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)
After sourcing Freesurfer, recon-all gives following error:
.../freesurfer/bin/recon-all: cannot execute: required file not found

Other functions, e.g. freeview, mri_info, all seem to work as expected

Would love some help.
Thanks,
Noam


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Re: [Freesurfer] Issue with mri_brainvol_stats for only some participants

[Huang, Yujing]

mri_brainvol_stats reads the following files:

mri/aseg.mgz
surf/lh.white
surf/rh.white
surf/lh.pial
surf/rh.pial
mri/brainmask.mgz
mri/transforms/talairach.xfm
$FREESURFER_HOME/ASegStatsLUT.txt

Can you check if they all exist for your subjects?

Any errors if you run 'mri_brainvol_stats ' at prompt?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Carly McIntyre-Wood
Sent: Tuesday, January 16, 2024 4:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Issue with mri_brainvol_stats for only some participants


External Email - Use Caution
Hi there,

I've come across a strange issue while running some new participants through 
Freesurfer 7.3.

A portion of participants (30%) are missing their stats files, although I have 
visually inspected the segmentation using Freeview and they look great. I have 
rerun autorecon3 and it only fixes the problem for select subjects. The exact 
error is below:


mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 
../surf/rh.thickness

   Update not needed

\n mri_brainvol_stats 1096 \n

Segmentation fault

I found one instance of this in the archives where someone recommended running:

recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 -wmparc 
-balabels

However, this command exits at the same point with the same error.

Thanks so much,
Carly
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Issue with mri_brainvol_stats for only some participants

[Huang, Yujing]

Can you attach recon-all.log of a failing subject?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Carly McIntyre-Wood
Sent: Tuesday, January 16, 2024 4:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Issue with mri_brainvol_stats for only some participants


External Email - Use Caution
Hi there,

I've come across a strange issue while running some new participants through 
Freesurfer 7.3.

A portion of participants (30%) are missing their stats files, although I have 
visually inspected the segmentation using Freeview and they look great. I have 
rerun autorecon3 and it only fixes the problem for select subjects. The exact 
error is below:


mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 
../surf/rh.thickness

   Update not needed

\n mri_brainvol_stats 1096 \n

Segmentation fault

I found one instance of this in the archives where someone recommended running:

recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 -wmparc 
-balabels

However, this command exits at the same point with the same error.

Thanks so much,
Carly
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Re: [Freesurfer] Midline white/pial surface

[Huang, Yujing]

Can you try the troubleshooting methods from this page:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Sunniva Fenn-Moltu
Sent: Monday, January 15, 2024 6:35 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Midline white/pial surface


External Email - Use Caution
Hi,

i'm running recon-all and have encountered an issue with the surface boundaries 
on several subjects. What I'm experiencing is that the midline surface is 
included in the white surface in one hemisphere, and in the pial surface on the 
other hemisphere. This results in the midline boundary of the thalamus and 
ventral DC being white surface in one hemisphere, and pial surface in the 
other. Do you have any idea why this is happening?
I am running freesurfer on NoMachine (freesurfer/7.4.1).

Best,
Sunniva

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Re: [Freesurfer] fsLR label to fsnative annotation

[Huang, Yujing]

Freesurfer .annot saves the annotation value at each vertex . The annotation is 
calculated from RGB in label file. Any labels with same RGB assigned will have 
the same annotations. They will appear to be the same label in .annot file.

Fix the label table in .gii, re-run mris_convert.

If you are running dev version, you can also fix RGB in separate LUT. Pass it 
to mris_convert -ctab  to replace the label table in .gii

Best,

Yujing




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bram Diamond
Sent: Monday, January 15, 2024 5:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] fsLR label to fsnative annotation


External Email - Use Caution
Dear FreeSurfer experts,

Happy new year! I hope you all are doing well!

I recently wrote the following question to the HCP-User Google Group and was 
directed to cross-post in the FreeSurfer list server by Dr. Matt Glasser.

I have created individualized rs-fMRI maps as dlabel fsLR 32k space using Kong 
et al. 
(2021)
 and I would like to resample them to a FreeSurfer annotation in anatomical 
space without losing individual parcel assignments. The method below resamples 
the maps but loses parcel assignments.

echo "running -cifti-seperate"
wb_command \
-cifti-separate \
$dlabel_in \
COLUMN \
-label CORTEX_LEFT 
$dlabel_dir/${dlabel_in_base_name}.L.fsLR_32k.label.gii \
-label CORTEX_RIGHT 
$dlabel_dir/${dlabel_in_base_name}.R.fsLR_32k.label.gii

for hemi in L R; do

gii_in=$dlabel_dir/${dlabel_in_base_name}.${hemi}.fsLR_32k.label.gii

sphere_in=$standard_dir/resample_fsaverage/fs_LR-deformed_to-fsaverage.${hemi}.sphere.32k_fs_LR.surf.gii

sphere_out=$standard_dir/resample_fsaverage/fsaverage_std_sphere.${hemi}.164k_fsavg_${hemi}.surf.gii

gii_out=$dlabel_dir/${dlabel_in_base_name}.${hemi}.fsaverage_164k.label.gii

area_in=$standard_dir/resample_fsaverage/fs_LR.${hemi}.midthickness_va_avg.32k_fs_LR.shape.gii

area_out=$standard_dir/resample_fsaverage/fsaverage.${hemi}.midthickness_va_avg.164k_fsavg_${hemi}.shape.gii

echo "running -label-resample for "$hemi""
wb_command \
-label-resample \
$gii_in \
$sphere_in $sphere_out \
ADAP_BARY_AREA \
$gii_out \
-area-metrics \
$area_in $area_out

hemilower=$(echo $hemi | tr '[:upper:]' '[:lower:]')
fshemi=${hemilower}h

annot_out=${out_dir}/${fshemi}.${dlabel_in_base_name}.fsaverage.annot

echo "running mri_convert for "$fshemi""
mris_convert \
--annot $gii_out \
$FREESURFER_HOME/subjects/fsaverage/surf/${fshemi}.pial 
\
$annot_out

echo "running mri_surf2surf"
mri_surf2surf \
--srcsubject fsaverage \
--trgsubject $sub_id \
--hemi $fshemi \
--sval-annot $annot_out \
--tval 
$SUBJECTS_DIR/$sub_id/label/${fshemi}.${dlabel_in_base_name}.${sub_id}.annot \
--sd ${SUBJECTS_DIR}

mri_segstats \
--annot $sub_id $fshemi 
Ind_parcellation_MSHBM_${sub_num}_w20_MRF5.${sub_id} \
--i $SUBJECTS_DIR/$sub_id/surf/${fshemi}.thickness \
--sum 
${out_dir}/${fshemi}.Ind_parcellation_MSHBM_${sub_num}_w20_MRF5.${sub_id}.thickness

done

The original dlabel has a parcel label table with the following column names, 
"KEY" (int, 0-400), "NAME" (string, detailed below), and "RED,
"GREEN," "BLUE," "ALPHA" for RGB/1 (image_1).

NAME is , where atlas is always "17networks," 
hemi is "LH" or "RH," network is one of 17 networks (e.g., "DefaultA"), region 
is ≥1 unique anatomical region for each network (e.g., "FPole" and "IPL" for 
"DafaultA"), and int is an integer ID for repeat parcels in the same network 
and region (e.g., "DefaultA_IPL_1" and "DefaultA_IPL_2").

However, when converted to a FreeSurfer annotation file using the method above, 
parcels are collapsed across  and the name is taken from the first 
instance (image_2).

For example, I have parcels "17networks_LH_DefaultA_IPL_1" and 
"17networks_LH_DefaultA_IPL_2" in the dlabel, but only a single label called 
"17networks_LH_DefaultA_IPL_1" includi

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

[Huang, Yujing]

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


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


External Email - Use Caution
Dear Yujing,

Thank you very much for your kind help.

So, you're saying I need more directive other than -qcashe?
My command was;

for d in Te* te* EPK* epk*

do recon-all -s $d -qcache

done



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

So, the command line looks like this?

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

I ran recon-all -qcashe not on the fsaverage folder, but in the SUBJECT_DIR.
In the previous post, I attached the wrong recon-all log (which was from 
fsaverage>scripts folder), but now I'm attaching the recon-all log file from a 
random subject folder.
Could you please look and check this recon-all as well?
Many thanks!

Best,
Asuka


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


Your recon-all command doesn't have the directive to tell it what to run. You 
also need to specify input files for your initial run.  See this wiki page for 
detail MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all<https://secure-web.cisco.com/11Bilsco5cPfi23kohUaJckmoejScJgxCVT9TueKMZWvsx7dAntYubRwWYXHtGKljKeBLeTqzQQ5UePuZUZnRFzxae5FFSuLRLH4HzelINkwLs96J8N2iaElEUM_9YKPg9etzBOD8OEAuG2UfdHxpyONcBHtLAn_f6EkrCSoSjzjNvXi_oX7KVCXXUF3o5g3Bjyz-ezPwcZ5YFtvqdbIYv52nG9qbUuOOaolTNutoq-ibvyTwQgNV48YK3yt4Hsi_B54h6NAIo1rBwTyHrWCfvL9-lF9ZVJPN9vRL5Pst33y1_GcnaQjVirIdC2QsnN3-/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all>



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



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



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



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



Best,



Yujing







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



External Email - Use Caution

Dear Freesurfer researchers,



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

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



I used the command below:

for d in Te* te* EPK* epk*

do recon-all -s $d -qcache

done



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

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

 recon-all -s subjectname -qcashe



(output from the terminal window)

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

If it is the case that there is a process running, you can kill it and start 
over or just let it run.

If the process has died, you should type:

 rm 
/media/m-proc/Vol03/FREESURFER7_SUBJECTS/teen_subject_name/scripts/IsRunning.lh+rh

**Try to copy the line and then rerun again with the quche code.



I'm currently using

freesurfer-x86_64-redhat-linux-gnu-dev4-20090216.



Do you have any ideas why the command did not produce different fwhm files?

I'm thinking about re-running the recon-all again, so I would appreciate it if 
you could help me modify the commands.

Thank you very much in advance.





Best regards,

Asuka


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Re: [Freesurfer] poor inferior cerebellum segmentation

[Huang, Yujing]

Here is an explanation of etiv calculation in Freesurfer - 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

etiv is not obtained via direct segmentation of all structures within the skull 
boundaries. Rather, its estimation depends on the linear transform between the 
T1 image and a T1w atlas.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Carlos Alcocer
Sent: Friday, January 5, 2024 4:11 PM
To: Freesurfer support list 
Subject: [Freesurfer] poor inferior cerebellum segmentation


External Email - Use Caution
Hello,

Inferior portion of cerebellum are not segmented well. It is included in 
skullstrip and I tried adding control points in cerebellar WM but this did not 
help. I am not interested in cerebellum but I do need eTIV. Will this poor 
cerebellar segmentation affect eTIV calculation?

Thank you,

Carlos


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

[Huang, Yujing]

Your recon-all command doesn't have the directive to tell it what to run. You 
also need to specify input files for your initial run.  See this wiki page for 
detail https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

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

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

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

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

Best,

Yujing



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


External Email - Use Caution

Dear Freesurfer researchers,



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

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



I used the command below:
for d in Te* te* EPK* epk*
do recon-all -s $d -qcache
done

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

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

 recon-all -s subjectname -qcashe



(output from the terminal window)
It could also be that recon-all was running at one point but died in an 
unexpected way.
If it is the case that there is a process running, you can kill it and start 
over or just let it run.
If the process has died, you should type:
 rm 
/media/m-proc/Vol03/FREESURFER7_SUBJECTS/teen_subject_name/scripts/IsRunning.lh+rh
**Try to copy the line and then rerun again with the quche code.


I'm currently using
freesurfer-x86_64-redhat-linux-gnu-dev4-20090216.

Do you have any ideas why the command did not produce different fwhm files?
I'm thinking about re-running the recon-all again, so I would appreciate it if 
you could help me modify the commands.
Thank you very much in advance.




Best regards,

Asuka

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Re: [Freesurfer] Subject does not have a bstampfile

[Huang, Yujing]

You need to specify the input files to process. Here is the wiki page for 
recon-all -  https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Best,

Yujing

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Joanna Kidon
Sent: Monday, January 8, 2024 3:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Subject does not have a bstampfile

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compute Segmentation of hippocampal subfields and nuclei of 
the amygdala (cross-sectional and longitudinal), as described on the 
https://secure-web.cisco.com/1thysYb_zO3z1vpgSTaPhhhrJHE6mFgjDwcJg3vFCVfZAwtvXgTVrtcAutSPTrtciZPyxNbynvc15Hs2QuWbY_5s83lqlEQoYQJki7l_TF3oztafbzs30sHpSw0h-eZSPjzJ5uVCT29lxgi-ynPEhcVbMEKprxj8oqXGxzhvsFrvGlrQlowS673v0V1k05awg3ja96pJZpAes0ADbo-3Cdp-F5Ia5oD5q7fabDh5N202LPH9PNC1ruPvKvy_5987OSpV7RTftXJev5hauvVESrxnACVsA0f5bGY-t55yLWz2a-Tkq1eIulXgNxAa228gMMBHaDYc4X4fiJjG0re3rdg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala,
but I get the following error when I run the recon-all -all -s command:

Subject does not have a bstampfile, copying 
/usr/local/freesurfer/7.3.2/build-stamp.txt
Subject FS Version: 
freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% 
fs-check-version match = 1 fs-check-version Done
INFO: SUBJECTS_DIR is /mnt/c/Users/GCM/Desktop/subjects Actual FREESURFER_HOME 
/usr/local/freesurfer/7.3.2 Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 
SMP Thu Oct 5
21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
#
#@# MotionCor Sun Jan  7 20:48:46 CET 2024
ERROR: no run data found in
/mnt/c/Users/GCM/Desktop/subjects/NowakG/mri. Make sure to have a volume called 
001.mgz in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: 
http://secure-web.cisco.com/1YoN1A69KdRcMav_4NI9T7PYgKG5FAtbmkvQ7vxtAUykGwuliarvPShgKfL_ItgaKWWnaYhDjK5FMWmDuPGEEEjW91LA3z7KDEeMiaIfV2jyXtfoUeeAjtPetkV6AuryGQBEKfk8d73IpHcgRIPrySwzLQaUtJT-A3dciz-Ma0n5qP4wsp5g9Tjvw5bGZUJlDFhJwWQrn04-RanD9XSLv0hlRr6ygjNO1BDIi4FgyjW3UWknkdWZwG9r4rG9cdS5Q0g6fBJ_QfVYe1DlgOs71lVji4Q7vMKZoWhEAgKq_5yhthldQEcJLHUmFLDrBcBX1TXcVwnrmkcLYG8z3GWHohA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FConversion
Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5
21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s NowakG exited with ERRORS at Sun Jan  7 20:48:46 CET 2024




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 
scripts/recon-all.log in case it's of any use.

Best regards,

Joanna


--
--
dr n.med., specjalista fizyki medycznej, neurobiolog Przewodnicząca Sekcji 
Diagnostyki Obrazowej Polskiego Towarzystwa Fizyki Medycznej Zakład Kardiologii 
Inwazyjnej i Elektrokardiologii, III Katedra Kardiologii Śląski Uniwersytet 
Medyczny w Katowicach Kierownik Działu Fizyki Medycznej, Koordynator ds. 
Ochrony Radiologicznej Z-ca Kierownika Zakładu Diagnostyki Obrazowej 
Górnośląskie Centrum Medycznego im. prof. L. Gieca SUM w Katowicach

PhD, specialist in medical physics, neurobiologist Chairwoman of the Diagnostic 
Imaging Section of the Polish Society of Medical Physics Department of Invasive 
Cardiology and Electrocardiology, 3rd Department of Cardiology, Medical 
University of Silesia in Katowice Head of the Medical Physics Department, 
Coordinator for Radiological Protection, Deputy Head of the Department of 
Diagnostic Imaging Leszek Giec Upper-Silesian Medical Centre of the Medical 
University of Silesia in Katowice

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Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

[Huang, Yujing]

This is from your recon-all.log
"
mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz 
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz

mri_convert: extra argument 
("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")
"

There is a space in your path to nii.gz. Can you remove the space by renaming 
the directory?

Also, your SUBJECTS_DIR points to your Freesurfer install directory - 
/usr/local/freesurfer/subjects. You might run into permission or symbolic link 
problems later. It is a good idea to set SUBJECTS_DIR to some other directory 
where you have write permissions.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Flemister, Abeoseh B.
Sent: Friday, January 5, 2024 3:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS


External Email - Use Caution
Hi FreeSurfer Team,

I am attempting to run recon-all on a 3T MRI image dataset. I used recon-all \ 
-all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and recon-all 
failed before completeing even the first step. I tried other files from our 
dataset and using .nii files and got the same result. I saw a recent thread 

 where someone's issue was improperly labeled WM lesions but my dataset is 
composed of healthy brains.

I attached my recon-all.logs. I am using a Linux virtual machine (FreeSurfer 
version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me 
know if you have any questions!

Thanks,
Abeoseh Flemister
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 .
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continue communication over unencrypted e-mail, please notify the sender of 
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mri_easyreg error: No cortical labels found; does the segmentation include cortical parcels?

[Huang, Yujing]

It looks like there are some extra characters before '-flo_seg' flag. The 
command line is split into 2 lines.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of r04458...@ntu.edu.tw
Sent: Wednesday, December 27, 2023 4:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_easyreg error: No cortical labels found; does the 
segmentation include cortical parcels?


External Email - Use Caution
Hello FreeSurfer Developers,

I'm attempting to run the mri_easyreg and I used the following command:

mri_easyreg --ref 
/home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1.nii
  --flo /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/r002_T1W.nii 
--ref_seg 
/home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1-1.nii
--flo_seg 
/home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/r002_T1W_synthseg.nii 
--flo_reg /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/r002_T1W.nii 
--fwd_field /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/FWF.nii.gz 
--bak_field /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/BWF.nii.gz 
--threads -1 --affine_only


  ERROR: Error: Floating segmentation must be provided --flo_seg: command not 
found

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.

1) FreeSurfer version: freesurfer_ubuntu22-7.4.1
2) Platform: Ubuntu 22.04.3 LTS

Please help me.
Thanks!
-Edward
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Re: [Freesurfer] recon all with optiBET brain mask

[Huang, Yujing]

This is from Freesurfer wiki -  MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ
Q. I have already skull-stripped data. Can I submit it to recon-all?
A: If your skull-stripped volume does not have the cerebellum, then no. If it 
does, then yes, however you will have to run the data a bit differently.
First you must run only -autorecon1 like this:
recon-all -autorecon1 -noskullstrip -s 
Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz 
and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this 
brainmask.mgz file and check that it looks okay (there is no skull, cerebellum 
is intact; use the sample subject bert that comes with your FreeSurfer 
installation to make sure it looks comparable). From there you can run the 
final stages of recon-all:
recon-all -autrecon2 -autorecon3 -s 
Hope it helps.
 Best,
Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of BALBONI Irene
Sent: Tuesday, December 19, 2023 3:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon all with optiBET brain mask


External Email - Use Caution
Hello,

I would like to run recon all on a batch of subjects using 2 inputs (mprage and 
mp2rage). I would also like to run recon all using as brain mask not the 
standard brain mask generated by recon-all itself but a previously created 
optiBET. Would you have any suggestion on how to proceed? I tried simply 
replacing the brainmask file with the optiBET but it did not work.
Just for context all my participants (150) have been already segmented using 
recon-all but we noticed during quality control that we still have skull 
stripping and pial surface errors for the majority of them and that is why we 
would like to implement the optiBET mask.

Thanks for your help,
Irene Balboni
PhD student
She/Her

Institute de 
plurilinguisme
 | Université de Fribourg
&
Brain and Language 
Lab
 | Université de Genève
c/o Campus Biotech
Chemin des Mines 9 – 1202
Université de Genève, CH
+41(0)223790141

Twitter
 | 
ResearchGate
 | 
Linkedin

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Re: [Freesurfer] Recon-all failing with pre-skullstripped input data (mri_em_register can't find brainmask.mgz)

[Huang, Yujing]

This is from Freesurfer wiki -  
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ
Q. I have already skull-stripped data. Can I submit it to recon-all?
A: If your skull-stripped volume does not have the cerebellum, then no. If it 
does, then yes, however you will have to run the data a bit differently.
First you must run only -autorecon1 like this:
recon-all -autorecon1 -noskullstrip -s 
Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz 
and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this 
brainmask.mgz file and check that it looks okay (there is no skull, cerebellum 
is intact; use the sample subject bert that comes with your FreeSurfer 
installation to make sure it looks comparable). From there you can run the 
final stages of recon-all:
recon-all -autrecon2 -autorecon3 -s 
Hope it helps.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of James Hengenius
Sent: Thursday, December 28, 2023 5:06 PM
To: Freesurfer support list 
Subject: [Freesurfer] Recon-all failing with pre-skullstripped input data 
(mri_em_register can't find brainmask.mgz)


External Email - Use Caution
Hello FS experts,

I downloaded some anatomical data. I have defaced full images and 
pre-skullstripped images for each participant. I tried the defaced images 
first, but FS skullstripping looks a little off (possibly because the defacing 
hides bits of the cranium in some images and causes problems in mri_watershed). 
So I would like to use the pre-skullstripped files as my initial inputs.

I have placed the pre-skullstripped file for each participant in 
$SUBJECTS_DIR/$subjid/mri/orig/. Each participant's skullstripped input volume 
is named 001.mgz.

I then submit the following command in a script to my slurm queue (after 
setting appropriate FS env vars), where the script input ${1} is the $subjid 
mentioned above:

recon-all \
-subject ${1} \
-all \
-openmp 40 \
-noskullstrip

The output log from FS ends with the following error. The function 
mri_em_register seems to be looking for brainmask.mgz, and fails to open it. If 
the input image is already extracted from the skull, do I need to manually call 
it brainmask.mgz rather than 001.mgz? Or am I missing something else in my 
function call (like order of flags)? Does -noskullstrip need to come before 
-openmp, for example?

Thanks!
Jim H.

End of recon-all output:

writing output to T1.mgz
3D bias adjustment took 1 minutes and 20 seconds.
@#@FSTIME  2023:12:28:16:07:04 mri_normalize N 7 e 80.39 S 0.66 U 102.70 P 128% 
M 581068 F 0 R 24411 W 0 c 32 w 229 I 0 O 0 L 1.00 1.38 9.22
@#@FSLOADPOST 2023:12:28:16:08:25 mri_normalize N 7 1.99 1.66 8.64
#-
#@# EM Registration Thu Dec 28 16:08:25 EST 2023
/gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri

 mri_em_register -uns 3 -mask brainmask.mgz nu.mgz 
/home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca
 transforms/talairach.lta

setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_em_register for OpenMP = 40 ==
reading 1 input volumes...
logging results to talairach.log
reading 
'/home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca'...
GCAread took 0 minutes and 1 seconds.
average std = 7.2   using min determinant for regularization = 5.2
0 singular and 884 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
error: 
mghRead(/gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri/brainmask.mgz,
 -1): could not open file^@
error: mri_em_register: could not open mask volume brainmask.mgz.
^@
@#@FSTIME  2023:12:28:16:08:25 mri_em_register N 7 e 1.42 S 0.25 U 1.43 P 118% 
M 446804 F 0 R 108260 W 0 c 2 w 56 I 0 O 0 L 1.99 1.66 8.64
@#@FSLOADPOST 2023:12:28:16:08:26 mri_em_register N 7 1.99 1.66 8.64
Linux nia0918.scinet.local 3.10.0-1160.102.1.el7.x86_64 #1 SMP Tue Oct 17 
15:42:21 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 1000108_20252_2_0 exited with ERRORS at Thu Dec 28 16:08:26 EST 
2023

For more details, see the log file 
/gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/scripts/recon-all.log
To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] aparcstats2table - append option

[Huang, Yujing]

'--append' option is added to aparcstats2table and asegstats2table. It should 
be available tomorrow in Freesurfer dev version.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Horn, Mitchell Jacob
Sent: Monday, December 18, 2023 9:06 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] aparcstats2table - append option

Exactly.

My understanding (and correct me if I'm wrong) is that both commands 
create/overwrite the specified --tablefile each time it's run.

Best,
Mitch


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Monday, December 18, 2023 8:55 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] aparcstats2table - append option

I would like to confirm that this is what you have in mind:

  1.  the new '-append' flag will work with '--tablefile=OUTPUTFILE'
  2.  when same OUTPUTFILE is specified, new stats output will be appended to 
the end of file

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Horn, Mitchell Jacob
Sent: Tuesday, December 12, 2023 10:10 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] aparcstats2table - append option

Hi FS Devs,

Would it be possible to add an "append" flag for use with aparcstats2table and 
asegstats2table? If I understand their usage correctly, each time one of them 
are run they will create (or overwrite) a new file. Not urgent but would be 
useful.

Thanks,
Mitch
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Re: [Freesurfer] aparcstats2table - append option

[Huang, Yujing]

I would like to confirm that this is what you have in mind:

  1.  the new '-append' flag will work with '--tablefile=OUTPUTFILE'
  2.  when same OUTPUTFILE is specified, new stats output will be appended to 
the end of file

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Horn, Mitchell Jacob
Sent: Tuesday, December 12, 2023 10:10 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] aparcstats2table - append option

Hi FS Devs,

Would it be possible to add an "append" flag for use with aparcstats2table and 
asegstats2table? If I understand their usage correctly, each time one of them 
are run they will create (or overwrite) a new file. Not urgent but would be 
useful.

Thanks,
Mitch
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Re: [Freesurfer] Convert Scanner RAS to Vertex RAS

[Huang, Yujing]

The conversions between  tkrRas and scannerRAS are as following in Freesurfer:

tkrRAS = tkrvox2ras * inv(vox2ras) * scannerRAS
scannerRAS = vox2ras * inv(tkrvox2ras) * tkrRAS

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Eric Tsang
Sent: Thursday, December 14, 2023 5:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Convert Scanner RAS to Vertex RAS


External Email - Use Caution
Dear All,
I have great deal of trouble converting scanner RAS to vertex RAS. I have 
tried a couple of formula (in the following) which had failed to produce 
accurate coordinate.

[tkR tkA tkrS] = [ScannerRAS 1] / (vox2ras * inv(tkrvox2ras))
[tkR tkA tkrS] = [ScannerRAS 1] * inv(vox2ras0)

Both of these formula produced distorted coordinates. Please help!

Thanks,
Tim
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Re: [Freesurfer] mri_error_no_clear_message

[Huang, Yujing]

Your recon-all was killed – “Command terminated by signal 9”.

Was your VM VirtualBox up and running the whole time?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fargol Rezayaraghi
Sent: Friday, December 15, 2023 3:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_error_no_clear_message


External Email - Use Caution
Hi FreeSurfer Team,
I hope this email finds you well.

I'm trying to use a T1 image to get the aparc+aseg and wmparc nifti files.

I was using this command:  recon-all -s Subject1 -i T1.nii - all -notal -check 
( I used recon-all -s Subject1 -i T1.nii - all first, and after getting 
Talairach error, I added -nota -check at the end).

I'm getting following messages without clear error number: recon-all -s 
Subject1 exited with ERRORS at Thu Dec 14 21:18:02 EST 2023
For more details, see the log file 
/home/developer/Desktop/freesurfer/7.2.0/subjects/Subject1/scripts/recon-all.log
To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

The version of the freesurfer: 
freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b

My platform is ubuntu 18_04_06 on Oracle VM VirtualBox

I've attached the log file.

--
Kind Regards,
Fargol R. Araghi (Rezayaraghi)
Ph.D. Candidate, University of Washington
Department of Mechanical Engineering
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
www.Kurtlab.com
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Re: [Freesurfer] Statistical Characteristics of Segmented Fornix from T1-w MR Images

[Huang, Yujing]

Can you try ‘mri_segstats’? It will compute statistics on segmented volumes  -  
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats

Yujing

From: Ahsan Ali 
Sent: Friday, December 15, 2023 10:57 AM
To: Freesurfer support list ; Huang, Yujing 
; Fischl, Bruce R.,PHD 
Subject: Re: [Freesurfer] Statistical Characteristics of Segmented Fornix from 
T1-w MR Images


External Email - Use Caution
Hi,

Sure.
I have used this command for segmentation: "recon-all -s name -i name.nii -all"

Then I used "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto_CCseg.mgz -f" 
command to estimate only fornix.

Now I have fornix.mgz file in which only one structure, fornix, is there. Now 
I'm interested to know the statistical values, such as fractal dimension and 
all.
I hope I have now conveyed my problem to you.

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

On Fri, Dec 15, 2023 at 7:31 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
Hi Ahsan,

Can you specify the commands that you have tried?

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Ahsan Ali
Sent: Thursday, December 14, 2023 11:02 PM
To: Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>>; 
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Statistical Characteristics of Segmented Fornix from T1-w 
MR Images


External Email - Use Caution
Dear Sir/Madam,

I have segmented T1-W MR images from the ADNI database using Freesurfer. From 
aseg.nii, I have estimated the fornix structure (label number 250). I tried 
many times to get the characteristics of these structures but couldn't. It 
would be helpful for me; kindly let me know.
File name "fornix.nii" at label 250. Its statistical parameters, such as 
fractal dimension, volume, mean, etc

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] Statistical Characteristics of Segmented Fornix from T1-w MR Images

[Huang, Yujing]

Hi Ahsan,

Can you specify the commands that you have tried?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ahsan Ali
Sent: Thursday, December 14, 2023 11:02 PM
To: Fischl, Bruce R.,PHD ; 
freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Statistical Characteristics of Segmented Fornix from T1-w 
MR Images


External Email - Use Caution
Dear Sir/Madam,

I have segmented T1-W MR images from the ADNI database using Freesurfer. From 
aseg.nii, I have estimated the fornix structure (label number 250). I tried 
many times to get the characteristics of these structures but couldn't. It 
would be helpful for me; kindly let me know.
File name "fornix.nii" at label 250. Its statistical parameters, such as 
fractal dimension, volume, mean, etc

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] cannot read nifti-2 files in freesurfer - files ok in AFNI

[Huang, Yujing]

Freesurfer only handles nifty-1 now.

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Patricia Pais Roldan
Sent: Thursday, December 14, 2023 8:17 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] cannot read nifti-2 files in freesurfer - files ok in AFNI


External Email - Use Caution

Dear Freesurfer team,

I am having problems reading files with nifti-2 header, the error I get is 
something like "error: No such file or directory; error: niiRead(): bad number 
of dimensions (31488) in $file*". I get this error with any FS function (e.g., 
with mri_info $file), so I cannot work with these files in FS at all. The 
original files were nifti-1 (and readable by FS) but after processing them in 
AFNI, they were converted to nifti-2 (and now FS cannot read them). I contacted 
the AFNI team and everything seems to be alright with the files (AFNI functions 
can work with them and they can be displayed in the AFNI viewer). Does FS have 
the requirement of files being nifti-1?

Thank you very much in advance.

Best regards,
Patricia




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] aparcstats2table - IndexError

[Huang, Yujing]

Can you check if you have any extra empty lines after your last ‘Input’?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Laura Willers de Souza
Sent: Thursday, December 14, 2023 3:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] aparcstats2table - IndexError


External Email - Use Caution
Hello FreeSurfer Developers,
I'm trying to get the cortical thickness values for a list of subjects using 
aparcstats2table and I'm encountering this error:

aparcstats2table --fsgd subjects.test1.fsgd --meas thickness --hemi lh 
--common-parcs --tablefile lh.aparc.thickness.table
SUBJECTS_DIR : /mnt/wsl/PHYSICALDRIVE1/FS_OUTPUTS
Traceback (most recent call last):
  File "/usr/local/freesurfer/7.4.1/python/scripts/aparcstats2table", line 376, 
in 
subj_listoftuples = assemble_inputs(options)
  File "/usr/local/freesurfer/7.4.1/python/scripts/aparcstats2table", line 273, 
in assemble_inputs
if splitline[0].upper() == 'INPUT':
IndexError: list index out of range

The fsgd file only contains the list of subjects, as illustrated below:
GroupDescriptorFile 1   
Title subjects.test1 
Input 002_S_0295_S13408
Input 002_S_0413_S13893
Input 002_S_0559_S14875

I have successfully executed the same command for an individual subject.
For other measurements (surface area, volume) this error also occurs.

It's worth noting that the images and files for the subjects and recon-all are 
stored on an external hard drive that I have mounted on Linux, emulated on 
Windows. Could this be the source of the problem?

I appreciate any assistance you can provide with resolving this issue.

Thanks in advance!

Laura Willers de Souza

PhD Student in Pharmacology and Therapeutics

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil
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Re: [Freesurfer] Automatic prompt reply for freesurfer subsegmentations

[Huang, Yujing]

>From what I understand, segmentBS.sh copies 'imagedump.mgz' from 
>$FREESURFER_HOME/average/BrainstemSS/atlas/AtlasDump.mgz. it then tries to 
>replace it with the image generated by mri_robust_register. All these happen 
>in Matlab using system(cp), and system(mv).  So, I think "mode 0444 
>(r--r--r--)" is a result of your system setting.

Can you check if your $FREESURFER_HOME/average/BrainstemSS/atlas/AtlasDump.mgz 
is read-only?

For the automatic prompt reply, you may find this helpful - 
https://www.baeldung.com/linux/bash-interactive-prompts

Best,

Yujing





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Gool, J.K. (Jari)
Sent: Tuesday, December 5, 2023 10:37 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Automatic prompt reply for freesurfer subsegmentations


External Email - Use Caution
Dear Yujing,

These are the rights I get when I cp a file within the proposed output 
directory: -rw-rw-r--.

Kind regards,

Jari Gool  |  MD-PhD candidate

Department of Anatomy & Neurosciences, Amsterdam UMC Location VUmc


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: vrijdag 24 november 2023 16:33
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Automatic prompt reply for freesurfer subsegmentations

In your terminal, after you copy a file, what are the permissions of the new 
file?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Gool, J.K. (Jari)
Sent: Friday, November 24, 2023 9:18 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Automatic prompt reply for freesurfer subsegmentations


External Email - Use Caution
Dear Yujing,

Thank you for the quick reply. When I enter umask in my terminal I already get 
0002 as output so I think this is not the issue. Is there anything else I could 
do?


Kind regards,

Jari Gool  |  MD-PhD candidate

Department of Anatomy & Neurosciences, Amsterdam UMC Location VUmc




Van: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 namens Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Verzonden: vrijdag 24 november 2023 13:59
Aan: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Onderwerp: Re: [Freesurfer] Automatic prompt reply for freesurfer 
subsegmentations


It looks like "imageDump.mgz" is copied to the directory during segmentation.



Can you check your 'umask'?

>umask



I think "mode 0444 (r--r--r--)" is caused by the umask setting to 0222. Try to 
change your umask to 0002 in .bashrc or .profile - add a line 'umask 0002'.



Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Gool, J.K. (Jari)
Sent: Thursday, November 23, 2023 6:33 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Automatic prompt reply for freesurfer subsegmentations



External Email - Use Caution

Dear,



I would like to run the different available Freesurfer subsegmentations 
(brainstem, amygdala/hippocampus, thalamus, hypothalamus and ScLimbic) on a 
large sample of 150 subjects (code below). I want to run multiple subjects in 
parallel using the sbatch command on the linux server I am working on. Because 
of previous recon-all processing in 7.3.2 I would like to also perform the 
subsegmentations in this version and ScLimbic in 7.4.0. The problem is that the 
"segmentBS.sh", "segmentThalamicNuclei.sh" and "segmentHA_T1.sh" halfway 
prompts for user input: "mv: replace 'imageDump.mgz', overriding mode 0444 
(r--r--r--)?". The imageDump.mgz file is made within this same subsegmentation 
script and I have no problem with replacing this file. When I run the code 
interactively I just reply with "y" and the subsegmentation finishes without 
any errors. When I want to submit my script as a job and in batch, I am unable 
to provide this user input and the subsegmentation gets stuck at the prompt. I 
have tried to change my code of the subsegmentations with yes and echo (such as 
"yes | segmentBS.sh ${subj}_ses-EEGfMRI1 
/home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/" or 
"echo "y" | segmentBS.sh ${subj}_ses-EEGfMRI1 
/home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/") but 
the script still gets stuck o

Re: [Freesurfer] Faces and vertices error !

[Huang, Yujing]

I think you need to specify ‘--src_type curv’ and ‘--trg_type curv’ to read 
thickness files.

It looks like you passed ‘thickness’ to the wrong flag. Use ‘—srcsurfval’ and 
‘—trgsurfval’ instead.

Here is wiki help page - https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2surf

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Sahil Bajaj
Sent: Wednesday, December 6, 2023 3:37 PM
To: Freesurfer support list 
Subject: [Freesurfer] Faces and vertices error !


External Email - Use Caution
Hi FreeSurfer community,

I am trying to map subject-specific cortical thickness map to standard 
fsaverage space and I ran the following command where sub1_filled is my 
individual subject in native:


mri_surf2surf --srcsubject sub1_filled --srcsurfreg thickness --trgsubject 
fsaverage --trgsurfreg thickness --hemi lh --sval sub1/surf/lh.thickness --tval 
fsaverage/surf/lh.thickness



After I run the above command, I am getting the following output and error. I 
am not sure how to resolve this and whether there is something wrong with my 
command line or with the data. I would greatly appreciate any help.



Source registration surface changed to thickness

Target registration surface changed to thickness



7.4.1



setenv SUBJECTS_DIR /Users/sbajaj/FS_Projects/

cd /Users/sbajaj/FS_Projects

mri_surf2surf --srcsubject sub1_filled --srcsurfreg thickness --trgsubject 
fsav1 --trgsurfreg thickness --hemi lh --sval sub1/surf/lh.thickness --tval 
fsav1/surf/lh.thickness



sysname  Darwin

hostname MDACM0CL9004107

machine  x86_64

user sbajaj

srcsubject = sub1_filled

srcval = sub1/surf/lh.thickness

srctype=

trgsubject = fsav1

trgval = fsav1/surf/lh.thickness

trgtype=

srcsurfreg = thickness

trgsurfreg = thickness

srchemi= lh

trghemi= lh

frame  = 0

fwhm-in= 0

fwhm-out   = 0

label-src  = (null)

label-trg  = (null)

OKToRevFaceOrder  = 1

UseDualHemi = 0

Reading source surface reg 
/Users/sbajaj/FS_Projects//sub1_filled/surf/lh.thickness

nquads=4456450,  nvertices=341

error: ERROR: MRISread: file 
'/Users/sbajaj/FS_Projects//sub1_filled/surf/lh.thickness' has many more faces 
than vertices!

Probably trying to use a scalar data file as a surface!
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Re: [Freesurfer] Segmentation error with T2w

[Huang, Yujing]

Hi Jakob,

I believe we fixed the bug in FS 7.4 release. Can you give it a try?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Litsch, Jakob Benjamin
Sent: Wednesday, December 6, 2023 10:40 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Segmentation error with T2w


External Email - Use Caution

Dear Freesurfer Team,
I am a master student from Berlin and pretty new to preprocessing MRI data, so 
please bear with me.

I am attempting to use Freesurfer as Part of my fMRIprep pipeline to preprocess 
patient data. When running fmriprep with only the T1w and the BOLD image it 
works fine. As soon as I put in my T2w image as well recon-all crashes at some 
point.
My patient data has lesions like brain tumors, just in case this could make 
freesurfer struggle.

Starting loop over 250145 vertices
   vno = 0, t = 5.16114
error: Numerical argument out of domain
error: MRIhistogramLabelRegion: constant image
error: Numerical argument out of domain
error: MRIhistogramLabelRegion: constant image
Segmentation fault

1) Freesurfer version:  freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
2) platform: Windows 11, Ubuntu 22.04.2 LTS (GNU/Linux 
5.15.133.1-microsoft-standard-WSL2 x86_64)
3) recon-all log: see attached

Looking forward to hear from you,
Jakob Litsch
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Re: [Freesurfer] Reopen issue 898: mri_binarize --replace misbehavior

[Huang, Yujing]

Hi,

‘mri_binarize –replace v1 v2’ performs transitive replacements if multiple 
‘–replace’ args are specified. This has been the behavior since May 25, 2021 
commit.

Now, new mri_binarize option '--no-transitive-replace' is introduced to turn 
off the transitive replacements. Let me know if this works for you. The changes 
should be available in Freesurfer dev version tomorrow.

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Lee Tirrell
Sent: Tuesday, November 28, 2023 8:19 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Reopen issue 898: mri_binarize --replace misbehavior


External Email - Use Caution
That could work in a simple case, but in a more complex case (10+ `--replace X 
Y` flags, for example) this would be more difficult to do. Also, then the 
ordering of the flags matter which adds more complication to constructing a 
command line call.

the workaround now would be to separate out into multiple `mri_binarize` 
commands if there are any overlap in labels, but the old behavior is preferable

On Wed, Nov 29, 2023 at 7:07 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:
Nick, what happens if you reverse the order (ie, do 15 72 first, then 11 15)?
On 11/28/2023 12:27 PM, Nick Schmansky wrote:

External Email - Use Caution

I have encountered the problem that 
chrisadamsonmcri
 describes in issue 
898.
 The last time I used mri_binarize was using FS v6, where it behaves like this:

mri_binarize --replace A B --replace B C

Label A would become B in the output.
Label B would become C in the output.

here's an example:

--replace 11 15 # map "4th Ventricle" -> "4th-Ventricle"\
--replace 15 72 # map "5th Ventricle" -> "5th-Ventricle"\

i want to convert a seg where the LUT maps 11 as 4th ventricle and 15 as 5th 
ventricle. i want to convert these to the FS LUT (using the replacements shown, 
15 and 72). But this results in 4th ventricle getting labeled as 5th ventricle! 
Four years ago i ran a script performing 230 replace functions to map 
Neuromorphometrics labels to FS, and it worked fine (evidenced by Dice testing 
and inspection). Today i ran the same script on the same data and get funky 
results on a half dozen or so structures that follow the example replacement 
scheme. My current workaround is to use mri_binarize from v6.


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Re: [Freesurfer] Converting register.dat file to reg.lta

[Huang, Yujing]

Src image is the movable image that is mapped to target image.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mirsol Choi
Sent: Wednesday, November 29, 2023 5:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Converting register.dat file to reg.lta


External Email - Use Caution
Hi Yujing,

Thanks again for your quick response.

For src image, do you mean the file that I used to generate the original 
register.dat file?
For instance, the register.dat file was produced by running dt_recon (using 
input of dti.nii.gz).

Is this dti.nii.gz for file I should use for correct conversion to reg.lta?

Thank you!
M

On Wed, Nov 29, 2023 at 3:40 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
Try to specify –src <> and –trg <>
--src
specify src image geometry (mov volume for TKREG/register.dat)
--trg
specify trg image geometry


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mirsol Choi
Sent: Wednesday, November 29, 2023 5:32 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Converting register.dat file to reg.lta


External Email - Use Caution
Hi Yujing,

I really appreciate your quick response.

The following is the error I get when I try to perform this:


Mirsols-MacBook-Pro:dtrecon mirsolchoi$ lta_convert --inreg register.dat 
--outreg reg.lta

7.4.1



--inreg: register.dat input TK REG transform.

--outreg: reg.lta output reg.dat matrix.

INFO: This REGISTER_DAT transform is valid only for volumes between  COR types 
with c_(r,a,s) = 0.

error: corRead(): can't open file 
/Users/mirsolchoi/Desktop/subjects/sub-001/dtrecon/COR-.info

ERROR readREG: cannot read src MRI

Mirsols-MacBook-Pro:dtrecon mirsolchoi$





Is there an additional file I need to complete this process?



Thank you so much for your time.



Mirsol

On Wed, Nov 29, 2023 at 3:24 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
You can try lta_convert.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mirsol Choi
Sent: Wednesday, November 29, 2023 5:19 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Converting register.dat file to reg.lta


External Email - Use Caution
Hello there,

I am wondering if there is a way to convert register.dat file produced from 
dt_recon to reg.lta. I need a reg.lta file that contains registration between 
the DTI data and processed (recon-all) T1 data.

I have tried to perform bbregister, but the alignment is completely off.

Thank you so much for your time!
Mirsol
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 .

Please note th

Re: [Freesurfer] Converting register.dat file to reg.lta

[Huang, Yujing]

Try to specify –src <> and –trg <>
--src
specify src image geometry (mov volume for TKREG/register.dat)
--trg
specify trg image geometry


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mirsol Choi
Sent: Wednesday, November 29, 2023 5:32 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Converting register.dat file to reg.lta


External Email - Use Caution
Hi Yujing,

I really appreciate your quick response.

The following is the error I get when I try to perform this:


Mirsols-MacBook-Pro:dtrecon mirsolchoi$ lta_convert --inreg register.dat 
--outreg reg.lta

7.4.1



--inreg: register.dat input TK REG transform.

--outreg: reg.lta output reg.dat matrix.

INFO: This REGISTER_DAT transform is valid only for volumes between  COR types 
with c_(r,a,s) = 0.

error: corRead(): can't open file 
/Users/mirsolchoi/Desktop/subjects/sub-001/dtrecon/COR-.info

ERROR readREG: cannot read src MRI

Mirsols-MacBook-Pro:dtrecon mirsolchoi$





Is there an additional file I need to complete this process?



Thank you so much for your time.



Mirsol

On Wed, Nov 29, 2023 at 3:24 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
You can try lta_convert.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mirsol Choi
Sent: Wednesday, November 29, 2023 5:19 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Converting register.dat file to reg.lta


External Email - Use Caution
Hello there,

I am wondering if there is a way to convert register.dat file produced from 
dt_recon to reg.lta. I need a reg.lta file that contains registration between 
the DTI data and processed (recon-all) T1 data.

I have tried to perform bbregister, but the alignment is completely off.

Thank you so much for your time!
Mirsol
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