[Freesurfer] Pial in the thalamus

[Yann Quidé]

Dear all,

We have this issue around the thalamus that is recurring in several of our 
scans and there does not seem to be a problem with the white matter mask in 
that area.

Is it a problem? Does anyone have an idea how to fix this? We are using 
Freesurfer v5.3.

Thanks.

Yann

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Re: [Freesurfer] Pial in the thalamus

[Yann Quidé]

Thanks Bruce, will try that!

Yann


> On 16 Mar 2017, at 10:39 AM, Bruce Fischl  wrote:
> 
> if you edit the aseg to make them thalamus and rerun autorecon2-wm and 
> autorecon3 it should fix it. Not sure why the aseg failed there though - it 
> usually does better
> cheers
> Bruce
> On Thu, 16 Mar 2017, Yann Quidé wrote:
> 
>> Hi Bruce,
>> 
>> Thanks for your reply. Most of the voxels are not labelled as thalamus on 
>> the aseg, only few partially cross the wm/pial lines (see screenshot 
>> attached).
>> Any recommendation?
>> 
>> Thanks.
>> 
>> Yann
>> 
>> 
>>> On 16 Mar 2017, at 1:24 AM, Bruce Fischl  wrote:
>>> 
>>> Hi Yann
>>> 
>>> are those voxels labeled thalamus in the aseg?
>>> 
>>> cheers
>>> Bruce
>>> On Wed, 15 Mar 2017, Yann Quidé wrote:
>>> 
>>>> Dear all,
>>>> 
>>>> We have this issue around the thalamus that is recurring in several of our 
>>>> scans and there does not seem to be a problem with the white matter mask 
>>>> in that area.
>>>> 
>>>> Is it a problem? Does anyone have an idea how to fix this? We are using 
>>>> Freesurfer v5.3.
>>>> 
>>>> Thanks.
>>>> 
>>>> Yann
>>>> 
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[Freesurfer] Problem with fsgd file

[Yann Quidé]

Dear all,I am sure it is something obvious, but I am stuck with that error.I am trying to analyse data and prepared my fsgd file, but when trying to use mri_glmfit, Terminal returns me the errorgdfReadHeader: reading group_age_sex.fsgdERROR: gdfRead: group_age_sex.fsgd is not formatted properly.  The first string is 'GroupDescriptorFile', should be 'GroupDescriptorFile'As you can read, I did not misspelled the GroupDescriptorFile and even added a 1 after! (as GroupDescriptorFile 1), as mentioned in the wiki.It does not seem to be any “useless" tab in the fsgd file. I have attached an exemple (I just left 1 subject)Thanks for your time.YannGroupDescriptorFile 1
Title BasicAnalysis  
Class 0  
Class 1  
Variables   Age  Sex 
Input   005 1   35  1___
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Re: [Freesurfer] Problem with fsgd file

[Yann Quidé]

Hi Douglas,

Thanks for looking at this. I am using FS 5.3 on a Mac OS 10.9 (Mavericks). If 
that helps, I wrote the initial file with TextWrangler.

Yann

> On 30 Mar 2017, at 7:18 am, Douglas N Greve  wrote:
> 
> I cannot replicate. What version of FS are you using and what platform 
> are you on?
> 
> 
> On 03/29/2017 04:01 PM, Yann Quidé wrote:
>> Dear all,
>> 
>> I am sure it is something obvious, but I am stuck with that error.
>> I am trying to analyse data and prepared my fsgd file, but when trying 
>> to use mri_glmfit, Terminal returns me the error
>> 
>> gdfReadHeader: reading group_age_sex.fsgd
>> 
>> ERROR: gdfRead: group_age_sex.fsgd is not formatted properly.
>> 
>>  The first string is 'GroupDescriptorFile', should be 
>> 'GroupDescriptorFile'
>> 
>> 
>> As you can read, I did not misspelled the GroupDescriptorFile and even 
>> added a 1 after! (as GroupDescriptorFile 1), as mentioned in the wiki.
>> 
>> It does not seem to be any “useless" tab in the fsgd file. I have 
>> attached an exemple (I just left 1 subject)
>> 
>> 
>> Thanks for your time.
>> 
>> 
>> Yann
>> 
>> 
>> 
>> 
>> 
>> 
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>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
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> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> 
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Re: [Freesurfer] Medial Surface Problem

[Yann Quidé]

Hi all,

We also have the same issue, any idea/suggestion?

Thanks.

Yann


> On 27 Apr 2017, at 9:43 am, Bronwyn Overs  wrote:
> 
> Hi Mailing List,
> 
> Still trying to solve the below medial surface problem. Does anyone have any 
> ideas?
> Kind regards,
> Bronwyn Overs
> Research Assistant
> 
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
> 
> neura.edu.au  <http://neura.edu.au/>
>  <https://twitter.com/neuraustralia> 
> <https://www.facebook.com/NeuroscienceResearchAustralia> 
> <http://www.neura.edu.au/help-research/subscribe>
>> On 28 Mar 2017, at 10:51 pm, Yann Quidé > <mailto:yannqu...@gmail.com>> wrote:
>> 
>> Dear all,
>> 
>> I have an equivalent issue with my data. Any idea on how to fix this?
>> 
>> Thanks.
>> 
>> Yann
>> 
>> 
>>> Begin forwarded message:
>>> 
>>> From: Bronwyn Overs mailto:b.ov...@neura.edu.au>>
>>> Subject: Re: [Freesurfer] Medial Surface Problem
>>> Date: 20 March 2017 10:28:37 am AEDT
>>> To: Freesurfer support list >> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>> Reply-To: Freesurfer support list >> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>> 
>>> Hello again mailing list,
>>> 
>>> Can anyone address the possible cause of the medial surface problem shown 
>>> below (overestimating of rh medial surface, shows up in the long image and 
>>> not the tp or base images). Forgot to mention that I am using freesurfer 
>>> v5.3 with an updated mris_make_surfaces binary (sourced from the 
>>> development version at 
>>> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/
>>>  
>>> <ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/>
>>>  ).
>>> 
>>> Here is the image again:
>>> 
>>> 
>>> Kind regards,
>>> Bronwyn Overs
>>> Research Assistant
>>> 
>>> Neuroscience Research Australia
>>> Margarete Ainsworth Building
>>> Barker Street Randwick Sydney NSW 2031 Australia
>>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
>>> 
>>> neura.edu.au  <http://neura.edu.au/>
>>>  <https://twitter.com/neuraustralia> 
>>> <https://www.facebook.com/NeuroscienceResearchAustralia> 
>>> <http://www.neura.edu.au/help-research/subscribe>
>>>> On 6 Mar 2017, at 1:17 pm, Bronwyn Overs >>> <mailto:b.ov...@neura.edu.au>> wrote:
>>>> 
>>>> Hi mailing list,
>>>> 
>>>> I am currently processing a longitudinal image and have come across a 
>>>> problem at the medial surface in the long image (step 3). As you can see 
>>>> in the attached image, the rh medial surface has been significantly 
>>>> overestimated and extends into the lh surface. This error showed up only 
>>>> in only 1 of the 2 long images for this subject, and both the time-point 
>>>> images and the base are perfectly fine. Do you know why this is happening? 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> Kind regards,
>>>> Bronwyn Overs
>>>> Research Assistant
>>>> 
>>>> Neuroscience Research Australia
>>>> Margarete Ainsworth Building
>>>> Barker Street Randwick Sydney NSW 2031 Australia
>>>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
>>>> 
>>>> neura.edu.au  <http://neura.edu.au/>
>>>>  <https://twitter.com/neuraustralia> 
>>>> <https://www.facebook.com/NeuroscienceResearchAustralia> 
>>>> <http://www.neura.edu.au/help-research/subscribe>
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>>>> 
>>>> 
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>>>> is
>>>> addressed. If you believe this e-mail was sent to you in error and the 
>>>> e-mail
>>>> contains patient information, please co

[Freesurfer] ROI extraction using functional masks

[Yann Quidé]

Dear FS experts,

I am trying to extract values for cortical thickness, surface area and volumes, 
from different functional ROIs. These cortical ROIs have been defined using SPM 
tools, and are in .nii format. My scans have been processed using FS v5.3.

Although the conversion seems to go well, the “end product” does not really 
look good, some of the extracted ROI for some subjects are empty. Does anyone 
have a clue of why?

Here is what I have done:

1) transform .nii file to .mgz file

$FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/L_ROI.mgz
$FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/R_ROI.mgz


2) to make sure our masks from SPM will match fsaverage templates, I did

tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/L_ROI.mgz -fthresh 0.5
tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/R_ROI.mgz -fthresh 0.5

It was fine.


3) I created a .dat file containing the registration matrix from avg152T1 onto 
fsaverage

cd $SUBJECTS_DIR/fsaverage/surf
spmregister --s fsaverage --mov $MASKS_DIR/avg152T1.nii --reg 
$REG_DIR/avg152T1_to_fsaverage.dat


4) Visualisation of the registration

tkregister2 --mov $MASKS_DIR/avg152T1.nii --targ 
$SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg 
$REG_DIR/avg152T1_to_fsaverage.dat --surf orig

The registration was bad, so… I manually relocate the TAL template onto the 
fsaverage template and saved a new avg152T1_to_fsaverage.dat file called 
avg152T1_to_fsaverage_edited.dat. This file is used for the next steps.


5) Visualisation of the registration of our mask onto fsaverage T1

cd $SUBJECTS_DIR/fsaverage/surf
tkmedit fsaverage T1.mgz \
  -overlay $MASKS_DIR/L_ROI.mgz \
  -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \
  -fthresh 0.5 \
  -surface lh.white -aux-surface rh.white 

tkmedit fsaverage T1.mgz \
  -overlay $MASKS_DIR/R_ROI.mgz \
  -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \
  -fthresh 0.5 \
  -surface lh.white -aux-surface rh.white 

Up to this sep, everything looks good.


6) Transformation of the ROI mask to surface and thickness

mri_vol2surf --src $MASKS_DIR/L_ROI.mgz --reg 
$REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi lh --o $MASKS_DIR/L_ROI.mgh
mri_vol2surf --src $MASKS_DIR/R_ROI.mgz --reg 
$REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi rh --o $MASKS_DIR/R_ROI.mgh

mri_cor2label --i $MASKS_DIR/L_ROI.mgh --surf fsaverage lh --id 1 --l 
$MASKS_DIR/L_ROI.label
mri_cor2label --i $MASKS_DIR/R_ROI.mgh --surf fsaverage rh --id 1 --l 
$MASKS_DIR/R_ROI.label


7) Extraction of the ROI surface and thickness for analyses

mris_anatomical_stats -l $MASKS_DIR/L_ROI.label -f 
$OUT_DIR/results_L_ROI_SubjID SubjID lh  
mris_anatomical_stats -l $MASKS_DIR/R_ROI.label -f 
$OUT_DIR/results_R_ROI_SubjID SubjID rh

Thanks to anyone who will be able to help me with that!

Yann
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[Freesurfer] Correction for multiple comparisons

[Yann Quidé]

External Email - Use Caution

Dear all,

Using Freesurfer 5.3, I would like to limit my whole-brain analyses to a mask I 
already defined (ie, small volume correction-like analysis).
To correct for multiple comparisons, I want to use the mri_glmfit-sim option. 
As I am looking within my own mask, I understand I need to run my own 
Monte-Carlo simulation. Would 10,000 permutations be sufficient?
Also, I am a bit confused on what is best practice when setting the cluster 
forming threshold. Should I use the mc-z=3 (that is p=0.001) or mc-z=1.3 (that 
is p=0.05)?
Here is an exemple of what I’m doing so far:

mri_glmfit-sim \
  --glmdir $STATS_DIR/lh.my_analysis.glmdir \
  --sim mc-z 1 3 mc-z.abs.3 \
  --sim-sign abs

Thanks for your time.

Yann

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Re: [Freesurfer] ROI extraction using functional masks

[Yann Quidé]

External Email - Use Caution

Hi Doug,

I apologise for the time I left this question unanswered… 
I have done some work on the issue, and discovered that the orientation was 
wrong (eg left ROI was on the right side), but this did not appear on step 2. 
Anyway, this is now fixed.

I have checked with Freeview how were the ROIs on ?h.white, and it looks pretty 
decent.

The whole pipeline seems to be working fine all the way, but for some subjects 
and for some ROIs, mris_anatomical_stats cannot extract anything!
I thought because I registered my ROIs on fsaverage, mris_anatomical_stats 
would be able to capture and extract teh average value within the ROI mask for 
all subjects? Is there anything I am missing here?

Any idea on what I could do to capture what is in my ROIs for all my subjects?

Thanks again for your time.

Yann



> On 16 Feb 2018, at 6:18 AM, Douglas N Greve  wrote:
> 
> At what step is the failure happening? Do the masks look ok on the surface?
> 
> 
> On 02/12/2018 08:06 PM, Yann Quidé wrote:
>> Dear FS experts,
>> 
>> I am trying to extract values for cortical thickness, surface area and 
>> volumes, from different functional ROIs. These cortical ROIs have been 
>> defined using SPM tools, and are in .nii format. My scans have been 
>> processed using FS v5.3.
>> 
>> Although the conversion seems to go well, the “end product” does not really 
>> look good, some of the extracted ROI for some subjects are empty. Does 
>> anyone have a clue of why?
>> 
>> Here is what I have done:
>> 
>> 1) transform .nii file to .mgz file
>> 
>> $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/L_ROI.mgz
>> $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/R_ROI.mgz
>> 
>> 
>> 2) to make sure our masks from SPM will match fsaverage templates, I did
>> 
>> tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/L_ROI.mgz -fthresh 0.5
>> tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/R_ROI.mgz -fthresh 0.5
>> 
>> It was fine.
>> 
>> 
>> 3) I created a .dat file containing the registration matrix from avg152T1 
>> onto fsaverage
>> 
>> cd $SUBJECTS_DIR/fsaverage/surf
>> spmregister --s fsaverage --mov $MASKS_DIR/avg152T1.nii --reg 
>> $REG_DIR/avg152T1_to_fsaverage.dat
>> 
>> 
>> 4) Visualisation of the registration
>> 
>> tkregister2 --mov $MASKS_DIR/avg152T1.nii --targ 
>> $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg 
>> $REG_DIR/avg152T1_to_fsaverage.dat --surf orig
>> 
>> The registration was bad, so… I manually relocate the TAL template onto the 
>> fsaverage template and saved a new avg152T1_to_fsaverage.dat file called 
>> avg152T1_to_fsaverage_edited.dat. This file is used for the next steps.
>> 
>> 
>> 5) Visualisation of the registration of our mask onto fsaverage T1
>> 
>> cd $SUBJECTS_DIR/fsaverage/surf
>> tkmedit fsaverage T1.mgz \
>>   -overlay $MASKS_DIR/L_ROI.mgz \
>>   -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \
>>   -fthresh 0.5 \
>>   -surface lh.white -aux-surface rh.white
>> 
>> tkmedit fsaverage T1.mgz \
>>   -overlay $MASKS_DIR/R_ROI.mgz \
>>   -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \
>>   -fthresh 0.5 \
>>   -surface lh.white -aux-surface rh.white
>> 
>> Up to this sep, everything looks good.
>> 
>> 
>> 6) Transformation of the ROI mask to surface and thickness
>> 
>> mri_vol2surf --src $MASKS_DIR/L_ROI.mgz --reg 
>> $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi lh --o $MASKS_DIR/L_ROI.mgh
>> mri_vol2surf --src $MASKS_DIR/R_ROI.mgz --reg 
>> $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi rh --o $MASKS_DIR/R_ROI.mgh
>> 
>> mri_cor2label --i $MASKS_DIR/L_ROI.mgh --surf fsaverage lh --id 1 --l 
>> $MASKS_DIR/L_ROI.label
>> mri_cor2label --i $MASKS_DIR/R_ROI.mgh --surf fsaverage rh --id 1 --l 
>> $MASKS_DIR/R_ROI.label
>> 
>> 
>> 7) Extraction of the ROI surface and thickness for analyses
>> 
>> mris_anatomical_stats -l $MASKS_DIR/L_ROI.label -f 
>> $OUT_DIR/results_L_ROI_SubjID SubjID lh
>> mris_anatomical_stats -l $MASKS_DIR/R_ROI.label -f 
>> $OUT_DIR/results_R_ROI_SubjID SubjID rh
>> 
>> Thanks to anyone who will be able to help me with that!
>> 
>> Yann
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>> 
>> 
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
>

[Freesurfer] Postdoctoral or experienced research position in a Neuroscience/Resilience/Twin Research Program

[Yann Quidé]

External Email - Use Caution

Posted on behalf of Dr Justine Gatt.



Dear Colleagues
 
Our team is currently advertising a postdoc / experienced research assistant 
position in a neuroscience research program focusing on wellbeing and 
resilience in twins. 
 
Applications close 28th September.
 
https://www.seek.com.au/job/37080366?_ga=2.13993015.160255953.1535437739-805767681.1383688706
 

 
I would appreciate if you could please circulate to your peers and colleagues.
 
Many thanks
Justine
 
 
Dr Justine M Gatt
Group Leader and Senior Research Scientist
Gatt Resilience Group
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
T +61 2 9399 1812
M PO Box 1165 Randwick Sydney NSW 2031 Australia
neura.edu.au 
School of Psychology
University of New South Wales
Randwick NSW 2052 Australia
psy.unsw.edu.au 

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[Freesurfer] Matlab runtime installation error for Freesurfer v7.1.0

[Yann Quidé]

External Email - Use Caution

Hi team,

I am trying to install fs_install_mcr R2014b, but encounter an error just at 
the end of it: 
mv: rename 
/var/folders/1f/4_zl7p9n795c2yq1dgb3hvt4gq/T/tmp.Xvv7Ku4d/install-target/v84
 to /Applications/freesurfer/7.1.0/MCRv84: Permission denied

Any idea how I can fix this to finalise the installation? I should have the 
admin rights on the machine.

Thanks,

Yann___
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Re: [Freesurfer] Matlab runtime installation error for Freesurfer v7.1.0

[Yann Quidé]

External Email - Use Caution

Ahah, yes that worked.

Thanks.

Yann


> On 11 Jun 2020, at 11:00 pm, Iglesias Gonzalez, Juan E. 
>  wrote:
> 
> It totally looks like you don’t 😉
> Did you rn the command as superuser (with sudo)?
>  
>  
> Juan Eugenio Iglesias
> Senior research fellow
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
> http://www.jeiglesias.com <http://www.jeiglesias.com/> 
>  
>  
>  
> From:  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Yann Quidé 
> mailto:yannqu...@gmail.com>>
> Reply-To: Freesurfer support list  <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Date: Thursday, June 11, 2020 at 06:16
> To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" 
> mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: [Freesurfer] Matlab runtime installation error for Freesurfer v7.1.0
>  
> External Email - Use Caution
> Hi team,
>  
> I am trying to install fs_install_mcr R2014b, but encounter an error just at 
> the end of it: 
> mv: rename 
> /var/folders/1f/4_zl7p9n795c2yq1dgb3hvt4gq/T/tmp.Xvv7Ku4d/install-target/v84
>  to /Applications/freesurfer/7.1.0/MCRv84: Permission denied
>  
> Any idea how I can fix this to finalise the installation? I should have the 
> admin rights on the machine.
>  
> Thanks,
>  
> Yann
> ___
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> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Re: [Freesurfer] Error recon-all mri_cc

[Yann Quidé]

External Email - Use Caution

Hi Doug,

Thanks for this. I sent the file; it’s called yannquide.tar.gz.

Yann

> On 16 Jun 2020, at 11:56 pm, Douglas N. Greve  wrote:
> 
> Can you upload the subject so I can take a look? Instructions below
> 
> 
> From the linux command line,
> Create the file you want to upload, eg, 
> cd $SUBJECTS_DIR
> tar cvfz subject.tar.gz ./subject
> Now log  into our anonymous FTP site:
> ftp surfer.nmr.mgh.harvard.edu <http://surfer.nmr.mgh.harvard.edu/>
> It will ask you for a user name: use "anonymous" (no quotes)
> It will ask you for a password: use "anonymous" (no quotes)
> cd transfer/incoming
> binary
> put subject.tar.gz
> Send an email that the file has been and the name of the file.
> 
> 
> 
> On 6/15/2020 8:28 PM, Yann Quidé wrote:
>> External Email - Use Caution
>> 
>> Hi there,
>> 
>> I am using Freesurfer v7.1.0 and encounter an error for few of my subjects 
>> only.
>> Recon-all finishes with errors, and it seems this occurs during the 
>> segmentation.
>> 
>> What can I do to fix this?
>> 
>> I attached the recon-all log for one of my subject.
>> 
>> Thanks,
>> 
>> Yann
>> 
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Re: [Freesurfer] Error recon-all mri_cc

[Yann Quidé]

External Email - Use Caution

Hi team,

I was just wondering if you received my file and if you had time to look at it?

Thanks,

Yann

> On 18 Jun 2020, at 7:08 am, Yann Quidé  wrote:
> 
> Hi Doug,
> 
> Thanks for this. I sent the file; it’s called yannquide.tar.gz.
> 
> Yann
> 
>> On 16 Jun 2020, at 11:56 pm, Douglas N. Greve > <mailto:dgr...@mgh.harvard.edu>> wrote:
>> 
>> Can you upload the subject so I can take a look? Instructions below
>> 
>> 
>> From the linux command line,
>> Create the file you want to upload, eg, 
>> cd $SUBJECTS_DIR
>> tar cvfz subject.tar.gz ./subject
>> Now log  into our anonymous FTP site:
>> ftp surfer.nmr.mgh.harvard.edu <http://surfer.nmr.mgh.harvard.edu/>
>> It will ask you for a user name: use "anonymous" (no quotes)
>> It will ask you for a password: use "anonymous" (no quotes)
>> cd transfer/incoming
>> binary
>> put subject.tar.gz
>> Send an email that the file has been and the name of the file.
>> 
>> 
>> 
>> On 6/15/2020 8:28 PM, Yann Quidé wrote:
>>> External Email - Use Caution
>>> 
>>> Hi there,
>>> 
>>> I am using Freesurfer v7.1.0 and encounter an error for few of my subjects 
>>> only.
>>> Recon-all finishes with errors, and it seems this occurs during the 
>>> segmentation.
>>> 
>>> What can I do to fix this?
>>> 
>>> I attached the recon-all log for one of my subject.
>>> 
>>> Thanks,
>>> 
>>> Yann
>>> 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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Re: [Freesurfer] Error recon-all mri_cc

[Yann Quidé]

External Email - Use Caution

Hi team,

I appreciate everyone is busy, but did anyone have time to look at my subject?
It was uploaded on June 18. It’s called yannquide.tar.gz

Thanks for your time.

Yann

> On 22 Jun 2020, at 12:51 pm, Yann Quidé  wrote:
> 
> Hi team,
> 
> I was just wondering if you received my file and if you had time to look at 
> it?
> 
> Thanks,
> 
> Yann
> 
>> On 18 Jun 2020, at 7:08 am, Yann Quidé > <mailto:yannqu...@gmail.com>> wrote:
>> 
>> Hi Doug,
>> 
>> Thanks for this. I sent the file; it’s called yannquide.tar.gz.
>> 
>> Yann
>> 
>>> On 16 Jun 2020, at 11:56 pm, Douglas N. Greve >> <mailto:dgr...@mgh.harvard.edu>> wrote:
>>> 
>>> Can you upload the subject so I can take a look? Instructions below
>>> 
>>> 
>>> From the linux command line,
>>> Create the file you want to upload, eg, 
>>> cd $SUBJECTS_DIR
>>> tar cvfz subject.tar.gz ./subject
>>> Now log  into our anonymous FTP site:
>>> ftp surfer.nmr.mgh.harvard.edu <http://surfer.nmr.mgh.harvard.edu/>
>>> It will ask you for a user name: use "anonymous" (no quotes)
>>> It will ask you for a password: use "anonymous" (no quotes)
>>> cd transfer/incoming
>>> binary
>>> put subject.tar.gz
>>> Send an email that the file has been and the name of the file.
>>> 
>>> 
>>> 
>>> On 6/15/2020 8:28 PM, Yann Quidé wrote:
>>>> External Email - Use Caution
>>>> 
>>>> Hi there,
>>>> 
>>>> I am using Freesurfer v7.1.0 and encounter an error for few of my subjects 
>>>> only.
>>>> Recon-all finishes with errors, and it seems this occurs during the 
>>>> segmentation.
>>>> 
>>>> What can I do to fix this?
>>>> 
>>>> I attached the recon-all log for one of my subject.
>>>> 
>>>> Thanks,
>>>> 
>>>> Yann
>>>> 
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> 

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Re: [Freesurfer] Error recon-all mri_cc

[Yann Quidé]

External Email - Use Caution

Hi Andrew,

Thanks for this.
Just a quick follow up question: does that mean I will have to recon all all 
the other scans that did not show this error with v7.1.1 for consistency, or 
will it be fine to keep them processed with v7.1.0?

Thanks,

Yann


> On 30 Jun 2020, at 2:04 am, Hoopes, Andrew  wrote:
> 
> Hi Yann (and anyone else with mri_cc failures on mac),
> We have a fix that we'll include in an upcoming 7.1.1 patch release. If you'd 
> like a quick local fix, you can update your distribution with the new version 
> of mri_cc by running the following commands (this might require sudo):
> cd $FREESURFER_HOME/bin
> rm mri_cc
> curl https://surfer.nmr.mgh.harvard.edu/pub/dist/tmp_patch/mri_cc 
> <https://surfer.nmr.mgh.harvard.edu/pub/dist/tmp_patch/mri_cc> -O mri_cc
> chmod +x mri_cc
> Please let us know if this does not solve your issue.
> Andrew
>  
> From:  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Yann Quidé 
> mailto:yannqu...@gmail.com>>
> Reply-To: FS Help  <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Date: Monday, June 29, 2020 at 2:35 AM
> To: FS Help  <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] Error recon-all mri_cc
>  
> External Email - Use Caution
> Hi team,
>  
> I appreciate everyone is busy, but did anyone have time to look at my subject?
> It was uploaded on June 18. It’s called yannquide.tar.gz
>  
> Thanks for your time.
>  
> Yann
> 
> 
>> On 22 Jun 2020, at 12:51 pm, Yann Quidé > <mailto:yannqu...@gmail.com>> wrote:
>>  
>> Hi team,
>>  
>> I was just wondering if you received my file and if you had time to look at 
>> it?
>>  
>> Thanks,
>>  
>> Yann
>> 
>> 
>>> On 18 Jun 2020, at 7:08 am, Yann Quidé >> <mailto:yannqu...@gmail.com>> wrote:
>>>  
>>> Hi Doug,
>>>  
>>> Thanks for this. I sent the file; it’s called yannquide.tar.gz.
>>>  
>>> Yann
>>> 
>>> 
>>>> On 16 Jun 2020, at 11:56 pm, Douglas N. Greve >>> <mailto:dgr...@mgh.harvard.edu>> wrote:
>>>>  
>>>> Can you upload the subject so I can take a look? Instructions below
>>>> 
>>>> 
>>>> From the linux command line,
>>>> Create the file you want to upload, eg, 
>>>> cd $SUBJECTS_DIR
>>>> tar cvfz subject.tar.gz ./subject
>>>> Now log  into our anonymous FTP site:
>>>> ftp surfer.nmr.mgh.harvard.edu <http://surfer.nmr.mgh.harvard.edu/>
>>>> It will ask you for a user name: use "anonymous" (no quotes)
>>>> It will ask you for a password: use "anonymous" (no quotes)
>>>> cd transfer/incoming
>>>> binary
>>>> put subject.tar.gz
>>>> Send an email that the file has been and the name of the file.
>>>> 
>>>> 
>>>> 
>>>> On 6/15/2020 8:28 PM, Yann Quidé wrote:
>>>>> External Email - Use Caution
>>>>> 
>>>>> Hi there,
>>>>> 
>>>>> I am using Freesurfer v7.1.0 and encounter an error for few of my 
>>>>> subjects only.
>>>>> Recon-all finishes with errors, and it seems this occurs during the 
>>>>> segmentation.
>>>>> 
>>>>> What can I do to fix this?
>>>>> 
>>>>> I attached the recon-all log for one of my subject.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Yann
>>>>> 
>>>>> ___
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>>  
>> 
>>  
> 
>  
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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[Freesurfer] Thalamic nuclei exited with ERRORS

[Yann Quidé]

External Email - Use Caution

Hi team,

I am trying to run the thalamic nuclei pipeline with FS7.3.2, on scans 
processed with recon-all from FS5.3 (mac OSX10.13).
However, I receive the below error.
Any idea how I could solve this?

Thanks in advance.

Yann

--
USER yann
HOST Ians-Mac-Pro.local
PROCESSID 86082 
PROCESSOR x86_64
OS Darwin
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 
Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 
13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64
--
freesurfer-darwin-macOS-7.3.2-20220804-6354275
 
setenv SUBJECTS_DIR 
/Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/Subjects
cd /Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/ENIGMA_BARI
/Applications/freesurfer/7.3.2/bin/segmentThalamicNuclei.sh sub-BA_IGP001

#
#@# Thalamic Nuclei processing Fri 19 Aug 2022 20:10:24 AEST
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/7.3.2/MCRv97//runtime/maci64:/Applications/freesurfer/7.3.2/MCRv97//bin/maci64:/Applications/freesurfer/7.3.2/MCRv97//sys/os/maci64:/Applications/freesurfer/7.3.2/lib/gcc/lib:
Invalid MEX-file 
'/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64':
 
dlopen(/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64,
 6): Symbol not found: chkstk_darwin
  Referenced from: 
/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64
 (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib
 in 
/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64

Error in kvlClear (line 11)

Error in SegmentThalamicNuclei (line 139)

MATLAB:mex:ErrInvalidMEXFile
Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 
13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64

Thalamic nuclei exited with ERRORS at Fri 19 Aug 2022 20:11:24 AEST






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Re: [Freesurfer] Thalamic nuclei exited with ERRORS

[Yann Quidé]

External Email - Use Caution

Not a good news for me, but thanks!

Yann

> On 20 Aug 2022, at 06:40, fsbuild  wrote:
> 
> Hello Yann,
> 
> It looks like the system library, /usr/lib/libSystem.B.dylib, is too old on 
> your machine running MacOS (10.13) to work with the Matlab MCRv97 runtime 
> environment.   MacOS 10.13 (High Sierra), 10.14 (Mojave) - are no longer 
> supported by Apple.  Soon Apple will also drop support for MacOS10.15 
> (Catalina).  I think you would need to upgrade to Catalina to use the Matlab 
> R2019b release as installed by the script ./freesurfer/bin/fs_install_mcr
> 
> - R.
> 
>> On Aug 19, 2022, at 07:33, Yann Quidé  wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> Hi team,
>> 
>> I am trying to run the thalamic nuclei pipeline with FS7.3.2, on scans 
>> processed with recon-all from FS5.3 (mac OSX10.13).
>> However, I receive the below error.
>> Any idea how I could solve this?
>> 
>> Thanks in advance.
>> 
>> Yann
>> 
>> --
>> USER yann
>> HOST Ians-Mac-Pro.local
>> PROCESSID 86082 
>> PROCESSOR x86_64
>> OS Darwin
>> ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 
>> Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 
>> 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64
>> --
>> freesurfer-darwin-macOS-7.3.2-20220804-6354275
>>  
>> setenv SUBJECTS_DIR 
>> /Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/Subjects
>> cd /Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/ENIGMA_BARI
>> /Applications/freesurfer/7.3.2/bin/segmentThalamicNuclei.sh sub-BA_IGP001
>> 
>> #
>> #@# Thalamic Nuclei processing Fri 19 Aug 2022 20:10:24 AEST
>> --
>> Setting up environment variables
>> ---
>> DYLD_LIBRARY_PATH is 
>> .:/Applications/freesurfer/7.3.2/MCRv97//runtime/maci64:/Applications/freesurfer/7.3.2/MCRv97//bin/maci64:/Applications/freesurfer/7.3.2/MCRv97//sys/os/maci64:/Applications/freesurfer/7.3.2/lib/gcc/lib:
>> Invalid MEX-file 
>> '/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64':
>>  
>> dlopen(/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64,
>>  6): Symbol not found: chkstk_darwin
>>   Referenced from: 
>> /private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64
>>  (which was built for Mac OS X 10.15)
>>   Expected in: /usr/lib/libSystem.B.dylib
>>  in 
>> /private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64
>> 
>> Error in kvlClear (line 11)
>> 
>> Error in SegmentThalamicNuclei (line 139)
>> 
>> MATLAB:mex:ErrInvalidMEXFile
>> Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 
>> 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64
>> 
>> Thalamic nuclei exited with ERRORS at Fri 19 Aug 2022 20:11:24 AEST
>> 
>> 
>> 
>> 
>> 
>> 
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>> https://secure-web.cisco.com/15LBal2C3-KL5Azu0J-sQfoobon70fBcSd_QYX72rH30sg9nH5VjErlsQC4AWdFZlozK6w7VzetIDEX8HlFBJaNwMDISKtctaOrJiM8TOuEQDsQNM72p-xaIHyQrccECl4QeC3vq_D8Mg_ZnyzxFMf1XogbXAZMu-C6S3eOKu-SduS5oSB3yneQlG5DE9hUb5qnW3HMi42yvSLJ4kmBtLzlG_nvWFFphTnrCamd1lRjTN5QqOV7VMx5Tu2JnIpEPGlP4aGTlO76cqyAz40SZHHsO_9_1Ie0ai1cwoLwfeY2fCswZv3brIqHphP5Zng8Z6/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 
> 

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Re: [Freesurfer] Thalamic nuclei exited with ERRORS

[Yann Quidé]

/7.2.0/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei
 sub-BA_105131 
/Volumes/MacintoshHD2/mridata/ASRB/ENIGMA_SZ_Thalamic_nuclei/Subjects 0.5 
/Applications/freesurfer/7.2.0/average/ThalamicNuclei/atlas/AtlasMesh.gz 
/Applications/freesurfer/7.2.0/average/ThalamicNuclei/atlas/AtlasDump.mgz 
/Applications/freesurfer/7.2.0/average/ThalamicNuclei/atlas/compressionLookupTable.txt
 0.05 L-BFGS v12 '/Applications/freesurfer/7.2.0/bin/fs_run_from_mcr 
/Applications/freesurfer/7.2.0/bin/' 1 0
134
Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 
13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64

Thalamic nuclei exited with ERRORS at Sat 27 Aug 2022 10:28:44 AEST



It seems that FS is looking for v84 files that are missing in v93?
Does anyone have an idea of what I am doing wrong?

Thanks in advance.

Yann


> On 20 Aug 2022, at 9:42 am, Yann Quidé  wrote:
> 
> Not a good news for me, but thanks!
> 
> Yann
> 
>> On 20 Aug 2022, at 06:40, fsbuild > <mailto:fsbu...@contbay.com>> wrote:
>> 
>> Hello Yann,
>> 
>> It looks like the system library, /usr/lib/libSystem.B.dylib, is too old on 
>> your machine running MacOS (10.13) to work with the Matlab MCRv97 runtime 
>> environment.   MacOS 10.13 (High Sierra), 10.14 (Mojave) - are no longer 
>> supported by Apple.  Soon Apple will also drop support for MacOS10.15 
>> (Catalina).  I think you would need to upgrade to Catalina to use the Matlab 
>> R2019b release as installed by the script ./freesurfer/bin/fs_install_mcr
>> 
>> - R.
>> 
>>> On Aug 19, 2022, at 07:33, Yann Quidé >> <mailto:yannqu...@gmail.com>> wrote:
>>> 
>>> External Email - Use Caution
>>> 
>>> 
>>> Hi team,
>>> 
>>> I am trying to run the thalamic nuclei pipeline with FS7.3.2, on scans 
>>> processed with recon-all from FS5.3 (mac OSX10.13).
>>> However, I receive the below error.
>>> Any idea how I could solve this?
>>> 
>>> Thanks in advance.
>>> 
>>> Yann
>>> 
>>> --
>>> USER yann
>>> HOST Ians-Mac-Pro.local
>>> PROCESSID 86082 
>>> PROCESSOR x86_64
>>> OS Darwin
>>> ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 
>>> Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 
>>> 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64
>>> --
>>> freesurfer-darwin-macOS-7.3.2-20220804-6354275
>>>  
>>> setenv SUBJECTS_DIR 
>>> /Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/Subjects
>>> cd /Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/ENIGMA_BARI
>>> /Applications/freesurfer/7.3.2/bin/segmentThalamicNuclei.sh sub-BA_IGP001
>>> 
>>> #
>>> #@# Thalamic Nuclei processing Fri 19 Aug 2022 20:10:24 AEST
>>> --
>>> Setting up environment variables
>>> ---
>>> DYLD_LIBRARY_PATH is 
>>> .:/Applications/freesurfer/7.3.2/MCRv97//runtime/maci64:/Applications/freesurfer/7.3.2/MCRv97//bin/maci64:/Applications/freesurfer/7.3.2/MCRv97//sys/os/maci64:/Applications/freesurfer/7.3.2/lib/gcc/lib:
>>> Invalid MEX-file 
>>> '/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64':
>>>  
>>> dlopen(/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64,
>>>  6): Symbol not found: chkstk_darwin
>>>   Referenced from: 
>>> /private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64
>>>  (which was built for Mac OS X 10.15)
>>>   Expected in: /usr/lib/libSystem.B.dylib
>>>  in 
>>> /private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64
>>> 
>>> Error in kvlClear (line 11)
>>> 
>>> Error in SegmentThalamicNuclei (line 139)
>>> 
>>> MATLAB:mex:ErrInvalidMEXFile
>>> Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 
>>> 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64
>>> 
>>> Thalamic nuclei exited with ERRORS at Fri 19 Aug 2022 20:11:24 AEST
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ___
>>> Freesurfer mai

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

[Yann Quidé]

External Email - Use Caution

Hi all,

Just bumping this one up.
Any help would be really appreciated.

Thanks in advance,

Yann

> On 27 Aug 2022, at 10:47 am, Yann Quidé  wrote:
> 
> Hi team,
> 
> I have been having troubles with processing my scans for thalamic subnuclei.
> In my previous post, I mentioned I was using FS7.3.2, but indeed realised 
> that this version was not fully compatible with my OS (OSX 10.13). So I 
> instead installed FS 7.2.0.
> However, I still have issues with the matlab runtime. I installed MCRv84, but 
> received the  error 
> 
> Setting ITK threads to 1
> #
> #@# Thalamic Nuclei processing Fri 26 Aug 2022 20:51:42 AEST
> --
> Setting up environment variables
> ---
> DYLD_LIBRARY_PATH is 
> .:/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64:/Applications/freesurfer/7.2.0/MCRv84//bin/maci64:/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64:/Applications/freesurfer/7.2.0/lib/gcc/lib:
> PostVMInit failed to initialize com.mathworks.mwswing.MJStartupForDesktop
> 
> 
>Segmentation violation detected at Fri Aug 26 20:51:49 2022
> 
> 
> Configuration:
>   Crash Decoding : Disabled
>   Current Visual : Quartz
>   Default Encoding   : ISO-8859-1
>   MATLAB Architecture: maci64
>   MATLAB Root: /Applications/freesurfer/7.2.0/MCRv84
>   MATLAB Version : 8.4.0.150421 (R2014b)
>   Operating System   : Darwin 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 
> 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64
>   Processor ID   : x86 Family 6 Model 44 Stepping 2, GenuineIntel
>   Software OpenGL: 0
>   Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java 
> HotSpot(TM) 64-Bit Server VM mixed mode
>   Window System  : Quartz
> 
> Fault Count: 1
> 
> 
> Abnormal termination:
> Segmentation violation
> 
> Register State (from fault):
>   RAX = 7ffa7100c000  RBX = 7ffa7100c000
>   RCX = 76c942d0  RDX = 0001142b897e
>   RSP = 7ffa7100c000  RBP = 9b6306c942d0
>   RSI = 7ffa70548690  RDI = 
> 
>R8 = 7ffa73834870   R9 = 7ffa7100c000
>   R10 = 00011e85f76a  R11 = 
>   R12 = 76c94330  R13 = 0001141063c7
>   R14 = 76c943a0  R15 = 00011e85f777
> 
>   RIP = 0001192a4f40  RFL = 7ffa73834870
> 
>CS = 9b6300305bc3   FS = 00011e85f76a   GS = 7ffa7100c1e8
> 
> Stack Trace (from fault):
> [  0] 0x000107349e64 
> /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwfl.dylib+00028260 
> _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052
> [  1] 0x00010734da2a 
> /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwfl.dylib+00043562 
> _ZN2fl4test17terminate_handledEv+0906
> [  2] 0x00010734d477 
> /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwfl.dylib+00042103 
> _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119
> [  3] 0x00010f5cbb7a 
> /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00387962 
> _Z32mnRunPathDependentInitializationv+3146
> [  4] 0x00010f5cbe58 
> /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00388696 
> _Z32mnRunPathDependentInitializationv+3880
> [  5] 0x00010f5c9733 
> /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00378675 
> mnFatalSignalHandler+0275
> [  6] 0x7fff5aad3f5a   
> /usr/lib/system/libsystem_platform.dylib+8026 _sigtramp+0026
> [  7] 0x76c9   
> +
> [  8] 0x0001140f7d67 
> /Applications/freesurfer/7.2.0/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679
>  jni_GetMethodID+0126
> [  9] 0x000112ab5271 
> /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwjmi.dylib+00160369 
> _Z12mljGetMethodP7_jclassPKcS2_+0049
> [ 10] 0x00011e0ba366 
> /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwhg.dylib+00598886 
> _ZN2ui14JavaScreenData20getPrimaryScreenRectEv+0150
> [ 11] 0x00011e0bfef4 
> /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwhg.dylib+00622324 
> _ZN10ScreenImpl13getScreenSizeEv+0036
> [ 12] 0x00011e0be2e2 
> /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwhg.dylib+00615138 
> _ZNK2ui24RootScreenAndPointerImpl13getScreenSizeEv+0018
> [ 13

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

[Yann Quidé]

External Email - Use CautionThanks for your help!I followed your instructions, but still have these issues.Actually, it seems to happen quite randomly, as I could process some subjects but not other, and also on subjects that I could previously process (I am using a loop for several subjects)!I attached logs from 1 subject for your information: for one the processing ran smoothly, for the others there are different errors….This seems very odd; do you have any idea what is going on?Java1.8 is installed on my machine, and linked with Matlab (R2018b), but it seems that the MCR is running its own version, and not sure how to update the MCR version of Java…Thanks again for your help.YannNote: the workaround from Matlab is to install some files from R2017b; my machine uses R2018b already, so not sure this is helpful.

log_segmentation_thalamus_fail1.log
Description: Binary data


log_segmentation_thalamus_fail2.log
Description: Binary data


log_segmentation_thalamus_success.log
Description: Binary data
On 30 Aug 2022, at 12:02 pm, fsbuild <fsbu...@contbay.com> wrote:MCRv84 looks like it should run on MacOS 10.13, so in a new terminal window, I would install it directly into the freesurfer distribution with,$ export FREESURFER_HOME=/Applications/freesurfer/7.2.0$ cd $FREESURFER_HOME$ rm -rf  MCRv84$ cd bin$ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2014bThen source the freesurfer setup script and try running things again to see if it works differently.The crash you listed looks like Matlab trying to run Java 1.7 which generates a segmentation fault.  There is a bug posting about this on The Mathworks web site, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://la.mathworks.com/matlabcentral/answers/697705-segmentation-violation-when-using-freesurfer-7-1-1-with-mcr-8-4   I do not have a login there to read the reply/workaround, but I do see postings that say a workaround is to run Matlab with the -nosplash flag at startup..If you still get a crash with Java 1.7, you could try adding java 1.8 to your machine, switch to running 1.8, and see if it works differently.  There should be a Java icon in the system preferences panel on your machine which might help you manage java on your machine.  You can download Java 1.8 from the oracle web site under the MacOS entry on MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.java.com/en/download/manual.jsp- R.On Aug 29, 2022, at 20:26, Yann Quidé <yannqu...@gmail.com> wrote:External Email - Use CautionHi all,Just bumping this one up.Any help would be really appreciated.Thanks in advance,YannOn 27 Aug 2022, at 10:47 am, Yann Quidé <yannqu...@gmail.com> wrote:Hi team,I have been having troubles with processing my scans for thalamic subnuclei.In my previous post, I mentioned I was using FS7.3.2, but indeed realised that this version was not fully compatible with my OS (OSX 10.13). So I instead installed FS 7.2.0.However, I still have issues with the matlab runtime. I installed MCRv84, but received the  error It seems that FS is looking for v84 files that are missing in v93?Does anyone have an idea of what I am doing wrong?Thanks in advance..YannOn 20 Aug 2022, at 9:42 am, Yann Quidé <yannqu...@gmail.com> wrote:Not a good news for me, but thanks!YannOn 20 Aug 2022, at 06:40, fsbuild <fsbu...@contbay.com> wrote:Hello Yann,It looks like the system library, /usr/lib/libSystem.B.dylib, is too old on your machine running MacOS (10.13) to work with the Matlab MCRv97 runtime environment.   MacOS 10.13 (High Sierra), 10.14 (Mojave) - are no longer supported by Apple.  Soon Apple will also drop support for MacOS10.15 (Catalina).  I think you would need to upgrade to Catalina to use the Matlab R2019b release as installed by the script ./freesurfer/bin/fs_install_mcr- R.On Aug 19, 2022, at 07:33, Yann Quidé <yannqu...@gmail.com> wrote:External Email - Use CautionHi team,I am trying to run the thalamic nuclei pipeline with FS7.3.2, on scans processed with recon-all from FS5.3 (mac OSX10.13).However, I receive the below error.Any idea how I could solve this?Thanks in advance.Yann--USER yannHOST Ians-Mac-Pro.localPROCESSID 86082 PROCESSOR x86_64OS DarwinITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Darwin Ians-Mac-Pro.local 17..7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64--freesurfer-darwin-macOS-7.3.2-20220804-6354275 setenv SUBJECTS_DIR /Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/Subjectscd /Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/ENIGMA_BARI/Applications/freesurfer/7.3.2/bin/segmentThalamicNuclei.sh sub-BA_IGP001##@# Thalamic Nuclei processing Fri 19 Aug 2022 20:10:24 

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

[Yann Quidé]

External Email - Use Caution

Thanks again for your help.
I tried with both R2017b and R2019b but no luck.
When I soft link either of these versions to MCRv84, I receive the following 
error:


sub-BA_IGP001
Setting ITK threads to 1
#
#@# Thalamic Nuclei processing Wed 31 Aug 2022 09:12:43 AEST
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64:/Applications/freesurfer/7.2.0/MCRv84//bin/maci64:/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64:/Applications/freesurfer/7.2.0/lib/gcc/lib:
dyld: lazy symbol binding failed: Symbol not found: 
__Z14standaloneMainRKSt6vectorISsSaISsEEbb
  Referenced from: 
/Applications/freesurfer/7.2.0/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei
  Expected in: 
/Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwlaunchermain.dylib

dyld: Symbol not found: __Z14standaloneMainRKSt6vectorISsSaISsEEbb
  Referenced from: 
/Applications/freesurfer/7.2.0/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei
  Expected in: 
/Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwlaunchermain.dylib

/Applications/freesurfer/7.2.0/bin/run_SegmentThalamicNuclei.sh: line 33: 49189 
Abort trap: 6   
/Applications/freesurfer/7.2.0/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei
 sub-BA_IGP001 /Volumes/MacintoshHD2/mridata/IGP/Subjects 0.5 
/Applications/freesurfer/7.2.0/average/ThalamicNuclei/atlas/AtlasMesh.gz 
/Applications/freesurfer/7.2.0/average/ThalamicNuclei/atlas/AtlasDump.mgz 
/Applications/freesurfer/7.2.0/average/ThalamicNuclei/atlas/compressionLookupTable.txt
 0.05 L-BFGS v12 '/Applications/freesurfer/7.2.0/bin/fs_run_from_mcr 
/Applications/freesurfer/7.2.0/bin/' 1 0
134
Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 
13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64

Thalamic nuclei exited with ERRORS at Wed 31 Aug 2022 09:12:45 AEST

For more details, see the log file 
/Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/scripts/thalamic-nuclei-mainFreeSurferT1.log

/Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.volumes.txt
/Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.mgz
/Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
.

If I use folders named MCRv93 or MCRv97, freesufer asks me to install R2014b…

Is there any other option?

Thanks in advance.

Yann

> On 31 Aug 2022, at 6:24 am, fsbuild  wrote:
> 
> One error in the logs is from missing symbols in the Matlab java library, and 
> another says to contact the Mathworks for technical support.  But Mathworks 
> is not going to support you because MacOS 10.13 does not meet the system 
> requirements for R2014b.
> 
> You don’t have to upgrade to MacOS 10.14 or 10.15 to run R2019b per 
> https://secure-web.cisco.com/1W8S3KSrnNfB7GaLAK6G1uuF5_rci5S4HvSmtU8OkqtOAlGdPsYx3jEm1z4Y7OmHeVtslmW-9uIZbPNIVgRvK0auH-mQsUSd_0q8QN4YPKjmGexCKIpvv-P0yefReTJqxWhMfLBcfcves8ir9RzBwOrSiaGI0pMlRnZScJYf35Jet-9xRV6-FDUduEe2WcQh8cceh3UsJbGSMj6Kk1ZHugtKo3wDqrpO221zNeVVcGR3ZP8q2pOJ63hj0ksourfzxewbP2QruVHmsWlvSZ5cEb1Tfi5YLscbi6lvf061m_DxCLSvTaqCt7WYONZLZ6CPkRIRjnA7-BlhaE9VqlcyRyg/https%3A%2F%2Fwww.mathworks.com%2Fcontent%2Fdam%2Fmathworks%2Fmathworks-dot-com%2Fsupport%2Fsysreq%2Ffiles%2Fsystem-requirements-release-2019b-macintosh.pdf
>  
> 
> - but the oldest version of MacOS you can run with R2019b is *exactly* MacOS 
> 10.13.6 and not an earlier version.  You should be able to use the MacOS 
> software update tool to update to 10.13.6 if you are not already running it. 
> I recommend that as I believe that is the last/most stable version of MacOS 
> 10.13.   From the compatibility chart, 
> https://secure-web.cisco.com/1kdVJWn7q7Z57Ogi3jAMS7tFUwuSagRqWDZlskobrq4cl1sACpVxcYANzfMNcuiIFixCe6sTjnWTT5u-L1AMA58ggKROWRK96WyFtIROUwgw-NTWSirLB5iqdf4mioDJxrsLO1VwKBvnARc_6LDlILK0reXDfIlCnGXYfnVKdEo-wEFEbteimCojgdl2Xxp6JKb_WpB_F4kvLBsg-fwrN7VE0lj4qw-dXWJOuoAxJ1Mxnknqqn6OTpckOngEt-UV378H6N8xQ7uHnXK77Ldf7b7Bbuyx3Cuf2-fDyVoJuT5kzEO8ghurIRk-JIe-NiAojL-Yxp4Hr2PrGdEXg4CF8ag/https%3A%2F%2Fwww.mathworks.com%2Fsupport%2Frequirements%2Fprevious-releases.html
>  
> 

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

[Yann Quidé]

External Email - Use Caution

Interesting… when I leave the folders named MCRv93 or MCRv97 (one at a time, 
not present together at the same time), then FS tells me I need to install 
MCRv84!
FS7.2.0 seems to only recognise MCRv84, hence why I used for example, sudo ln 
-s v93 MCRv84.
(I kept folders stored and named v93 and v97 in FREESURFER_HOME, so that I can 
work with them, if I used v93 I rename it MCRv93)
When using MCRv84, the segmentation violation only happens for some subjects, 
independently of if they have been successfully processed with the thalamic 
subfield script in the past or not.

This is so odd, I am really lost here!

Thanks again for your help.

Yann

> On 31 Aug 2022, at 1:24 pm, fsbuild  wrote:
> 
> After you install either R2017b or R2019b using the fs_install_mcr script you 
> should end up with either ./freesurfer/MCRv9.3 or ./freesurfer/MCRv9.7   
> There are no soft links to create manually and there should be no references 
> to MCRv8.4 in DYLD_LIBRARY_PATH or in the shell environment.
> 
> - R.
> 
> 

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Re: [Freesurfer] Thalamic nuclei exited with ERRORS

[Yann Quidé]

External Email - Use Caution

This is the error I get when for example, I use MCRv93

sub-BA_IGP001
 
ERROR: cannot find Matlab 2014b runtime in location:
 
/Applications/freesurfer/7.2.0/MCRv84
 
It is looking for either: 
  bin/glnxa64/libmwlaunchermain.so(Linux 64b) or
  bin/maci64/libmwlaunchermain.dylib (Mac 64b)
 
The hippocampal/amygdala and brainstem modules require the (free) Matlab 
runtime.
You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2014b.
To do so, please run the following command (you might need root permissions):
 
fs_install_mcr R2014b
 
For further details, please visit 
https://secure-web.cisco.com/1aVhobXpwrsVvrcVPxB9MI-BKvtQCINTnExZQSgdCNRja1gSU-env7ES67-lBNCfvXZM3Da229ux5SydG78FBuFmypy1M0wxB6VpPfk7I8PRKLvGgdJG735qZdDFKESihHN39DBr-_Ke7RCrTMOd_-72hQFJFHz__31alWI-JDV8p8TXKrRD1xmePfdqJDyhNHcQf10aOkK5WuOGXcX4VoiuejItFBmiaR1vtsxXJLS197g219t2vLRSrxTyp3NBmB7wAVER2fZES4_B0G5U8hp0j8QVNi7Dqw09f-_mWxtdGhI-2JsUjUXpO8qPd4-t6/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMatlabRuntime
 
/Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.volumes.txt
/Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.mgz
/Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
.

Yann

> On 31 Aug 2022, at 1:51 pm, fsbuild  wrote:
> 
> It’s possible something in 7.2.0 still requires MCRv84.  If so, it is 
> probably not going to work to use a soft link to fake out the name, and using 
> a different version of Matlab run time could explain the crashes.  Please 
> send along the output showing MCRv84 is required.
> 
> - R.
> 
> 

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Re: [Freesurfer] Thalamic nuclei exited with ERRORS

[Yann Quidé]

External Email - Use Caution

Hi again,

Just wanted to confirm the randomness of the issue… and see if there was any 
potential explanation for this.

I decided to go back from scratch, using a copy of my scans processed with 
FS5.3.
I re-ran the thalamic nuclei pipeline from FS7.2.0 a first time: 3 subjects 
only (out of 139) were actually processed for thalamic nuclei.
I ran it a second time (did not change any parameter), “excluding" the 3 scans 
that were processed in the previous round (deleted from a text file I call to 
identify my subjects), and got 2 new scans to be processed; these 2 were not 
processed in the previous round, giving me the segmentation violation error!
I am currently running a third round (minus the previous 5 scans), and at least 
1 new scan is being processed…. that sent an error at the 2 previous round.

Any idea of what could go wrong? 

Thanks for your time.

Yann

> On 31 Aug 2022, at 2:12 pm, Yann Quidé  wrote:
> 
> This is the error I get when for example, I use MCRv93
> 
> sub-BA_IGP001
>  
> ERROR: cannot find Matlab 2014b runtime in location:
>  
> /Applications/freesurfer/7.2.0/MCRv84
>  
> It is looking for either: 
>   bin/glnxa64/libmwlaunchermain.so(Linux 64b) or
>   bin/maci64/libmwlaunchermain.dylib (Mac 64b)
>  
> The hippocampal/amygdala and brainstem modules require the (free) Matlab 
> runtime.
> You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2014b.
> To do so, please run the following command (you might need root permissions):
>  
> fs_install_mcr R2014b
>  
> For further details, please visit 
> https://secure-web.cisco.com/1iHk6T6OBHrbNMB24br5MdKlQzlWpJc9EKeEEEWfb83XfMZNGLZlNDf_C94nMo-BGlBDTHzq-uenqgExMJzSMxCkpy8UXx9M_E3LKgK1YvKPdZXqe741pw2e1vMl9SnnqoJMzU8KczGbLwq_xDm-Th_sZppO0z28c15TDv8QgzBl_VIr2BfO3LQr3i-8oYepIUkuGdwnFw-giMjOa2yz3HLN5WTX0GIG2XpigmIk278UwRJDF4DYSYdptvTVAtCR4ssdaw-FsZNSWZXGx_rX1y2SriVzesQcY7Vx5GhzNBZluKcGYQHsVBfdZnUyYHMdP/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMatlabRuntime
>  
> <https://secure-web.cisco.com/1iHk6T6OBHrbNMB24br5MdKlQzlWpJc9EKeEEEWfb83XfMZNGLZlNDf_C94nMo-BGlBDTHzq-uenqgExMJzSMxCkpy8UXx9M_E3LKgK1YvKPdZXqe741pw2e1vMl9SnnqoJMzU8KczGbLwq_xDm-Th_sZppO0z28c15TDv8QgzBl_VIr2BfO3LQr3i-8oYepIUkuGdwnFw-giMjOa2yz3HLN5WTX0GIG2XpigmIk278UwRJDF4DYSYdptvTVAtCR4ssdaw-FsZNSWZXGx_rX1y2SriVzesQcY7Vx5GhzNBZluKcGYQHsVBfdZnUyYHMdP/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMatlabRuntime>
>  
> /Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.volumes.txt
> /Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.mgz
> /Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
> .
> 
> Yann
> 
>> On 31 Aug 2022, at 1:51 pm, fsbuild > <mailto:fsbu...@contbay.com>> wrote:
>> 
>> It’s possible something in 7.2.0 still requires MCRv84.  If so, it is 
>> probably not going to work to use a soft link to fake out the name, and 
>> using a different version of Matlab run time could explain the crashes.  
>> Please send along the output showing MCRv84 is required.
>> 
>> - R.
>> 
>> 
> 

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Re: [Freesurfer] mri_sclimbic_seg patch issue?

[Yann Quidé]

External Email - Use Caution

Hi all,

I have the same issue on Ubuntu 22.04, patch is installed.
Many thanks,

Yann 

> On 20 Dec 2022, at 04:29, daedalu...@aol.com wrote:
> 
> External Email - Use Caution
> 
> 
> Dear FreeSurfer Developers,
> 
> We are interested in implementing " mri_sclimbic_seg " from FreeSurfer 7.3.2 
> and are having trouble getting it to finish processing.
> 
> When I tried to run mri_sclimbic_seg. I keep getting a python error and the 
> process never finishes. I searched through the forum and it said that this 
> was a known error and that there was a patch. When I installed the patch I 
> got the exact same error.
> 
> The error message is: “ValueError: operands could not be broadcast together 
> with shapes (4,) (3,)”
> The link to the forum post is:
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
> claiming to be 
> https://secure-web.cisco.com/1AOO2G3Y9tIa3C9R7SheXdTmfFlIb7ZE6S7sOyW05Pn5KgUixvaLbdD9R1S6_Zi3KZjHAxNtpCZE3cPPjsACbaj0MP4zQqxSVGDRjTV8yfBtix-5EBxDDM_u2DGLzEPfKHNrV4jtEvpXA7sKFoxeMQ8XnpvNXlnaNbUityY1bkGrb7RK49FccouDavh7x8l2DNWz-w00BObPqu2ZP7CSfM5W5DffZk5ZiDpMH8GCh_WApOI6SwGuqz90fE2YtOFT2hjq3BMCI6Uyut8rMbXgLh38CxtmF5PXbBQREWN6aF5kqZFfB05KyviFvQALJWJ-Tl_T1E6eUQAgjiJv1_Ws3eg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg73652.html
>  
> 
>  
> We tried running it on the test subject “bert” just to make sure the issue is 
> not with our test scan and I got the same error.
> 
> We are getting the error even after installing the patch.  Here are the 
> details of the command line I used to run it and the error message:
>  
> Command line:
> mri_sclimbic_seg --s bert --o 
> /usr/local/freesurfer/7.3.2-1/subjects/bert/mri/mri_sclimbic_seg.mgz 
> --write_volumes --write_qa_stat
>  
> Error:
> Traceback (most recent call last):
>   File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
> 1049, in 
> main()
>   File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
> 232, in main
> segmenter.process_files(**params)
>   File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
> 578, in process_files
> post, seg, vox_counts, volumes, mean_probs = self.segment(image)
>   File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
> 498, in segment
> conformed = self.preprocess(image)
>   File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
> 490, in preprocess
> processed = image.conform(shape=(*self.inshape, self.nchannels), 
> voxsize=1.0, orientation='RAS', dtype='float32', copy=False)
>   File 
> "/usr/local/freesurfer/7.3.2-1/python/lib/python3.8/site-packages/surfa/image/framed.py",
>  line 574, in conform
> conformed = conformed.reshape(shape, copy=False)
>   File 
> "/usr/local/freesurfer/7.3.2-1/python/lib/python3.8/site-packages/surfa/image/framed.py",
>  line 515, in reshape
> delta = (np.array(shape) - np.array(self.baseshape)) / 2
> ValueError: operands could not be broadcast together with shapes (4,) (3,)
>  
> 
> We are beginning to study professional and amateur fighters, and we suspect 
> that shearing/disruptions to the septum pellucidum may have downstream 
> consequences to the connectivity/DTI measures in the septal nuclei, mammilary 
> bodies, etc.
> 
> Thanks in advance for any help or comments you can provide.
> 
> Sincerely
> 
> -Randy
> 
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