[Freesurfer] Passcode request for Freesurfer virtual machine

2022-11-28 Thread Gillian Grennan 
External Email - Use Caution

Hi,

I am a graduate student at the University of Washington. I am trying to
download the FS_7_2_0_Ubuntu_18_04_06.ova.7z but was prompted for a
password. Could I get access to this password?

Best,
Gillian
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[Freesurfer] Pass code request for Freesurfer virtual machine

2022-11-28 Thread Eduardo Europa 
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Hello,

I would like to follow up on my request to receive the pass code for the
Freesurfer virtual machine: FS_7_2_0_Ubuntu_18_04_06.ova.7z

Thank you,

*Eduardo Europa, PhD, CCC-SLP (he/him)*
Assistant Professor, Communicative Disorders & Sciences
San José State University
eduardo.eur...@sjsu.edu
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Re: [Freesurfer] VM password

2022-11-28 Thread fsbuild 
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Hello Eyesha,
The password was (re)sent to your email about ~30 minutes ago - please check 
your spam filters.
The password is for the VM itself and not tied to the machine hosting the VM.
- R.

On Nov 28, 2022, at 20:04, Eyesha Younus eyeshayou...@gmail.com 
wrote:External Email - Use 
CautionHello,I need a 
passwordto install the VM.Is this password tied to an email address 
or to a machine?The reason I ask thisis because I need to install the VM 
on two computers; one personal and one 
work.Thanks___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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Re: [Freesurfer] Permission denied error

2022-11-28 Thread fsbuild 
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Hello Adam,
I hope you saw the previous email I sent you about changing SUBJECTS_DIR to be 
different from the default.  Just wondering if you did that for 
SUBJECTS_DIR before running the recon-all.
- R.

On Nov 23, 2022, at 23:13, Adam Tartaglia aetartag...@gmail.com 
wrote:External Email - Use 
CautionHello,Immediately after 
running recon-all, I get an error that says cannot create directory, permission 
denied. I am not sure as to why this is happening. My license is in the correct 
location.Thank you for your time,- 
Adam___Freesurfer mailing 
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[Freesurfer] VM password

2022-11-28 Thread Eyesha Younus 
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Hello,
I need a password to install the VM.
Is this password tied to an email address or to a machine?
The reason I ask this is because I need to install the VM on two computers;
one personal and one work.

Thanks
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[Freesurfer] New subscriber

2022-11-28 Thread Eyesha Younas 
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Sending my email to become able to post to the forum.
Thanks 

Sent from my iPhone

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Re: [Freesurfer] recon-all failing to generate wm surface

2022-11-28 Thread Huang, Yujing 
Hi Christopher,

I noticed that you were only running 'recon-all -autorecon1 -autorecon2'. I 
don't think ?h.white surface are generated for the command combinations. 
'recon-all -all' will run all recon steps and generate ?h.white.

Here is a description of recon-all process and flags:
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Best,

Yujing


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Christopher Mcnorgan
Sent: Wednesday, November 23, 2022 5:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all failing to generate wm surface


External Email - Use Caution
A student and I have independently been trying to reconstruct a dataset. We've 
tried it a couple different ways using either an additional FLAIR or a T2 image 
and always hit a point where the process halts because of a missing surface 
file:

Loading lh.white surf
error: No such file or directory
error: MRISread(/home/cpmcnorg/VMP/FS_002/surf/lh.white): could not open file

This has happened when running just the autorecon1 step or both autorecon1 and 
autorecon2. I'm using freesurfer 7.2.0 on a linux computer, and my student is 
running 7.3.2 on a Mac. In my most recent test, I ran
recon-all -autorecon1 -autorecon2 -i  -T2  
-subjid 
and I have several surface files (e.g., ?h.orig and even ?h.white.preaparc) but 
not the ?h.white surface. I'm unclear what's causing the recon-all script to 
look for the wm surface before it's been created.
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[Freesurfer] TRACULA: domainname: Command not found.

2022-11-28 Thread Ward Deferm 
External Email - Use Caution

DearFreesurfer developers,


when trying to run trac-all -prep I am running into this error


gbw-d-m0128:DIFFUSION r0755008$ trac-all -prep -c 
/Users/r0755008/Desktop/mri_data/TRACULA/TRACULA_CONFIGURATION_FILE.txt

domainname: Command not found.

Too many ('s.

ERROR: Syntax error in configuration file 
/Users/r0755008/Desktop/mri_data/TRACULA/TRACULA_CONFIGURATION_FILE.txt


I checked the file but there seem to be no errors in the ('s.


This error has previously been encountered 
https://secure-web.cisco.com/1sKX4EXSdl-lzzKBfb369ful1KJMpWkExgYjXUfdMyAgEiLxmN-7MUWuEnZfe6fFIgowB68U2mNgao0KjS4PAfFLRsTmh7OkFg6D4IV4CMi-68OueIKNIDatn-hDv1YZ15W7tXz_fi2msIxxR_qP6YQk4asNuiMw9V9LHaembEzvAAr-oMUyw8yw_mrwjKGcR189BLip2OKFKDJS1qiS9UVHptmlDleX7ja_VsDq6QHHrrE2n0R8vFbYXAM1IkF6tbv6cfSKV91f3sbBxrvJgl16Yba47czO4agSUB9yuP0UTkvcJfaHXzQ6nM7-r0Xvq/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg70662.html%23
 but there is no solution proposed for the facts that the domainname command is 
missing from my mac in the /usr/bin folder. What can i do to solve this error. 
In the attachments you can find the tracula config file if this would be 
helpful. Thank you for the help.



Kind regards,



Ward Deferm






# T1 images and FreeSurfer segmentations are expected to be found here

setenv SUBJECTS_DIR /Users/r0755008/Desktop/mri_data/STRUCT

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /Users/r0755008/Desktop/mri_data/TRACULA

# Subject IDs
# Here each subject is listed twice because it has two diffusion scans
#
set subjlist = (NT001 \
NT001 \ 
NT002 \
NT002 \ 
NT003 \
NT003 \ 
NT004 \
NT004 \ 
NT005 \
NT005 \ 
NT006 \
NT006 \ 
NT007 \
NT007 \ 
NT009 \
NT009 \ 
NT010 \
NT010 \ 
NT011 \
NT011 \ 
NT012 \
NT012 \ 
NT013 \
NT013 \ 
NT014 \
NT014 \ 
NT015 \
NT015 \ 
NT016 \
NT016 \ 
NT017 \
NT017 \ 
NT018 \
NT018 \ 
NT020 \
NT020 \ 
NT021 \
NT021 \ 
NT024 \
NT024 \ 
NT025 \
NT025 \ 
NT026 \
NT026 \ 
NT027 \
NT027 \ 
NT028 \
NT028 \ 
NT029 \
NT029 \ 
NT030 \
NT030 \ 
NT032 \
NT032 \ 
NT033 \
NT033 \ 
NT034 \
NT034 \ 
NT035 \
NT035 \ 
NT036 \
NT036 \ 
NT037 \
NT037 \ 
NT038 \
NT038 \ 
NT039 \
NT039 \ 
NT040 \
NT040 \ 
PT002 \
PT002 \
PT003 \
PT003 \
PT004 \
PT004 \
PT005 \
PT005 \
PT007 \
PT007 \
PT008 \
PT008 \ 
PT010 \
PT010 \ 
PT011 \
PT011 \
PT013 \
PT013 \
PT014 \
PT014 \
PT015 \
PT015 \
PT016 \
PT017 \
PT018 \
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PT020 \
PT020 \
PT021 \
PT021 \
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PT023 \
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PT036 \
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PT037 \
PT037 \
PT038 \
PT038 \
PT039 \

Re: [Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

2022-11-28 Thread Douglas N. Greve 
that is quite strange. Does it happen every time? What is the 
mri_glmfit-sim command line and terminal output?

On 11/23/2022 2:47 PM, Vicente Ferrer wrote:
>  External Email - Use Caution
>
> Dear Freesurfer users,
>
> I was trying yo use mri_glmfit-sim after using mri_glmfit that run 
> successfully and I encounter this error:
>   
>
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>
>
> 
>  ERROR: READ THIS -
> --vv-
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
> If you seek help with this problem, make sure to send:
>1. Your command line:
>  mri_glmfit --C 
> /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/tmp.mri_glmfit-sim-29440/contrast_moca_groups.mtx
>  --sim perm 1000 1.5 
> /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_b  
> br.FA_Avg.corr_g_glmdir/csd/perm.th15.abs.j001 --sim-sign abs --fwhm 0 --fsgd 
> /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd
>  dods --mask /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg  
> 16_syn_bbr.FA_Avg.corr_g_glmdir/mask.mgh --y 
> /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/eres.mgh
>  --perm-force --seed 1669778971
>2. The terminal output of this program (ie, everything it prints to the 
> screen)
>3. The FSGD file 
> (/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd)
>4. The design matrix (null)/Xg.dat
> Attempting to diagnose further
> SumSq: Min=1.455099 (col 24), Max=8.657582 (col 23)
>   ... could not determine the cause of the problem
> --
>
> Seems like there is a problem with the condition matrix, but I do not 
> understand why. Could you help me with this problem? I attached the contrast 
> and fsgd files
>
> Best,
> Vicente Ferrer
> Predoctoral Researcher BCBL
> http://secure-web.cisco.com/1kWZEOu8GTFhJvEwUHVoEpHYRwVtjwPjaW-68jFXGIsKvsccvtZ_SpRT4mbfMn9yTEj2SS5sODMuPyTAI7wxqhCmRxBRJ-35S_I8dxkyBkn-mSO5ejNKj3y_fRHlzfZYF0Y7e4avfl65oYvF1P9f6zlpO9fvp61CMx3UMDUkUt33HANwhKrNAQrsy2Y5VCcoRrA2AKBS0Z5P-jUa88tp7dylA1Zd2jmD5f7dpneDGC1UTgcKCSiQESkTtkx8M29TK78bxICiS2DYkMxYTENKlkex0JPgoayYX8JXmUgwvPcKnzKLxI-NITvFv7ql7vHrpEha80-krYMT5O5ictU2HZA/http%3A%2F%2Fwww.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: 
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Re: [Freesurfer] Editing the coregistration

2022-11-28 Thread Douglas N. Greve 
you can just rerun preproc-sess. it will see that the reg file has 
changed. As a precaution, I would change the permissions of that file to 
read-only, otherwise it could get overwritten (not likely, but possible)


On 11/21/2022 7:45 PM, Asa Borzabadi Farahani wrote:


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Hi,
I hope this email finds you well.

I am doing slab imaging and when I run preproc-sess command to do the 
functional preprocessing, the results of co-registration are not 
optimal, hence I need to do manual editing and save a new 
transformation file.


After that, should I run the preproc-sess with option -regfile again? 
if not, what is the solution.


Regards,
Asa Farahani

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Re: [Freesurfer] recon-all failing to generate wm surface

2022-11-28 Thread Douglas N. Greve 

please send the recon-all.log file

On 11/23/2022 5:10 PM, Christopher Mcnorgan wrote:


External Email - Use Caution

A student and I have independently been trying to reconstruct a 
dataset. We've tried it a couple different ways using either an 
additional FLAIR or a T2 image and always hit a point where the 
process halts because of a missing surface file:


Loading lh.white surf
error: No such file or directory
error: MRISread(/home/cpmcnorg/VMP/FS_002/surf/lh.white): could not 
open file


This has happened when running just the autorecon1 step or both 
autorecon1 and autorecon2. I'm using freesurfer 7.2.0 on a linux 
computer, and my student is running 7.3.2 on a Mac. In my most recent 
test, I ran
recon-all -autorecon1 -autorecon2 -i  -T2 file> -subjid 
and I have several surface files (e.g., ?h.orig and even 
?h.white.preaparc) but not the ?h.white surface. I'm unclear what's 
causing the recon-all script to look for the wm surface before it's 
been created.


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Re: [Freesurfer] Confirming FSGD Format and Contrasts

2022-11-28 Thread Douglas N. Greve 

yes, that should work. make sure to use DOSS.

On 11/23/2022 11:50 AM, Olivier Brown wrote:


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Dear FreeSurfer experts,

I would like to confirm my FSGD file format and mtx contrasts prior to 
continuing with my analyses. Here is some background information: I 
have two groups (treatment, control) and would like to determine 
whether our quantitative scale, CDRISC, is associated with thickness 
within each group. I would like to control for sex, handedness, and 
age. Seeing as sex and handedness are categorical, I entered them as 
Classes instead of variables (Controlleftmale was not included, as no 
participant fell in that group).



GroupDescriptorFile 1   
Title CDRISC  
Class Controlrightfemale   
Class Controlleftfemale   
Class Treatrightfemale
Class Treatleftfemale
Class Controlrightmale 
Class Treatrightmale 
Class Treatrightmale
Variables   CDRISC_TREATMENT   CDRISC_CONTROL   age 
Input sub-1 Controlrightfemale  0 1910.66
Input sub-2 Controlleftfemale   0 2614
Input sub-3 Treatrightmale  35 014.02
Input sub-4 Treatleftmale   35 010.16
[...]


My contrasts (DOSS) are as follows:

[Nregressors = Nclasses + Nvariables
Nregressors = 7 + 3
Nregressors = 10]

Treatment CDRISC slope = 0 0 0 0 0 0 0 1 0 0
Control CDRISC slope = 0 0 0 0 0 0 0 0 1 0


Are there any glaring issues with this model? The only extra step of 
consideration here is that I have yet to demean the data. Any guidance 
is appreciated.


Warm regards,
Olivier Brown


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[Freesurfer] R: SAMSEG Lesion images not written

2022-11-28 Thread Cerri, Stefano 
Great!

You can use the command "samseg" with the flag "--recon" instead of 
"run_samseg". This will first run SAMSEG to obtain a whole-brain segmentation, 
then recon-all will use this segmentation to perform surface analysis and 
cortical parcellation -- instead of using ASEG segmentation. Look at the help 
function for more information.

Stefano

Da: Giulio Siracusano 
Inviato: domenica 27 novembre 2022 10:07
A: Cerri, Stefano 
Cc: freesurfer@nmr.mgh.harvard.edu 
Oggetto: Re: [Freesurfer] SAMSEG Lesion images not written


External Email - Use Caution

Hi Stefano,
I've got this thanks. I simply use freeview and ingest region-specific .mgz 
files.

I just wanted to understand one thing.
I realize that using SAMSEG or ASEG it is possible to obtain subcortical 
segmentation (44 parameters are visualized, representing different regions).
I realized that fusiform gyrus, middle temporal and entorhinal cortex volumes 
cannot be derived using one of the above mentioned methods.
I just wanted to know if is there any way to achieve cortical parcellation 
without using ASEG?
Or, in alternative, is there a way to estimate fusiform gyrus, middle temporal 
and entorhinal cortex volumes from the variables obtained in samseg.stats?

Hope to be clear

Giulio Siracusano






On Sun, 27 Nov 2022 at 14:22, Cerri, Stefano 
mailto:sce...@mgh.harvard.edu>> wrote:
Hi Giulio,

I'm not sure I understand what your goal is. Are you just trying to visualize 
specific brain structures over your input image? Are you interested in 
segmentation maps or binary segmentations?

If you want to visualize segmentation maps, you can just use Freeview and load 
the specific structure file(s). Note that these segmentation maps are 1) not 
binary, i.e., they have values *between* 0 and 1, and 2) they are in the same 
space as your input image.

If you want to visualize binary segmentation for specific structures you can do 
this in Freeview. You load your segmentation (seg.mgz) as a lookup table and 
select only the label values that you're interested in.

Hope it helps,
Stefano

Da: Giulio Siracusano 
mailto:giuliosiracus...@gmail.com>>
Inviato: domenica 27 novembre 2022 04:01
A: Cerri, Stefano mailto:sce...@mgh.harvard.edu>>; 
freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Oggetto: Re: [Freesurfer] SAMSEG Lesion images not written


External Email - Use Caution

Hi Stefano,
I'd like to ask you a question wrt SAMSEG.
I'd like to extract segmentation maps using SAMSEG, and I know already that we 
have to use '--save-posteriors' option when running the command.

They will be saved in the samseg output directory under the "posteriors" folder.

How is it possible, starting from these binary segmentation maps, creating 
multiple images of the brain where a given (segmentated) region is highlighed?
In order to do that, you have to multiply a given reference brain images -over- 
each segmentation map (which is a binary matrix with 0's and 1's).
What is the reference brain image all these segmentation maps are related to?

I hope to be clear enough

Best regards
Giulio Siracusano

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Re: [Freesurfer] Ubuntu 7z Password Requst

2022-11-28 Thread RW :D 
External Email - Use Caution

 To Whom It May Concern:
I am requesting the password for the FS_7_2_0_ubuntu_18_04_06.ova.7z file so 
that I can extract the .ova file. I would really appreciate it if you could 
send it to me!

Thank you so much!
Sincerely,Rebecca Wu
On Tuesday, November 22, 2022 at 03:46:03 PM EST, RW :D 
 wrote:  
 
 To Whom It May Concern:
I am requesting the password for the FS_7_2_0_ubuntu_18_04_06.ova.7z file so 
that I can extract the .ova file. I would really appreciate it if you could 
send it to me!

Thank you so much!
Sincerely,Rebecca Wu
   
   -


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[Freesurfer] R: SAMSEG Lesion images not written

2022-11-28 Thread Cerri, Stefano 
Hi Giulio,

I'm not sure I understand what your goal is. Are you just trying to visualize 
specific brain structures over your input image? Are you interested in 
segmentation maps or binary segmentations?

If you want to visualize segmentation maps, you can just use Freeview and load 
the specific structure file(s). Note that these segmentation maps are 1) not 
binary, i.e., they have values *between* 0 and 1, and 2) they are in the same 
space as your input image.

If you want to visualize binary segmentation for specific structures you can do 
this in Freeview. You load your segmentation (seg.mgz) as a lookup table and 
select only the label values that you're interested in.

Hope it helps,
Stefano

Da: Giulio Siracusano 
Inviato: domenica 27 novembre 2022 04:01
A: Cerri, Stefano ; freesurfer@nmr.mgh.harvard.edu 

Oggetto: Re: [Freesurfer] SAMSEG Lesion images not written


External Email - Use Caution

Hi Stefano,
I'd like to ask you a question wrt SAMSEG.
I'd like to extract segmentation maps using SAMSEG, and I know already that we 
have to use '--save-posteriors' option when running the command.

They will be saved in the samseg output directory under the "posteriors" folder.

How is it possible, starting from these binary segmentation maps, creating 
multiple images of the brain where a given (segmentated) region is highlighed?
In order to do that, you have to multiply a given reference brain images -over- 
each segmentation map (which is a binary matrix with 0's and 1's).
What is the reference brain image all these segmentation maps are related to?

I hope to be clear enough

Best regards
Giulio Siracusano
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Re: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

2022-11-28 Thread Andrew Beaudin 
External Email - Use Caution

Hi Huang,
  Thank you very much for your help with this.  Apologies for the delay.

  You should be able to retrieve sample images from the following link (expires 
on Dec. 2).  I have also included a brief word document at the link that 
includes some details of the nifti images.

https://secure-web.cisco.com/1Ey_DY3jZ8b1bW8m_xwPzSRElxfKGmEgDwV0bkOmCuHK0Kmxdv7PKs6Jf0G7VgjddMANZwnWTUhEkpcXnNc-96yDxI3bWzeA0Shj-XSErS9IAKrfDc7rNvVFPk1gthZEdOQwpsO2ftHEeDdRcRMhPtE95Sbr66ryahiNvWcOGsE6LnyqWNwEsbH-NScaHhp7-dhJJBNI9XYicWZirFUE05sqtmsy6i7TC_38L5ZnmXAHJ2lL-aYYsZN8LW07dvy4pvWHQn2yvnif3YyGhux-QTUVMa9dF5CbSsGe4tMj0cuCKDHH1sLW_P7kXdQLhcN-H2DAwyCRCvjoxORFabjtSKXHEXY65fDl6SnKXtM_emps/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ


The command call I am using is:

mri_robust_template --mov 2001A_T1o_brain.nii.gz 2001B_T1o_brain.nii.mgz --lta 
2001A2template.lta 2001B2template.lta --average 1 --template 
2001_template.nii.gz --satit


  However, while troubleshooting I have also tried the following with no 
success:

1) using the --iscale flag - same MyMatrix::RotationMean Error (see below for 
log)
2) using --inittp 0 - results in a 'Segmentation fault'
3) using --average 0 - same MyMatrix::RotationMean Error
4) using Freesurfer v7.2 - same MyMatrix::RotationMean Error
5) running mri_robust_template call on Catalina and Big Sur systems with FS 
v6.0 - same MyMatrix::RotationMean Error.


Again, thank you for the help….and please let me know if your need any 
additional information or anything clarified.

Andrew

Andrew Beaudin, PhD | Postdoctoral Scholar
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273

From: Huang, Yujing 
Sent: November 22, 2022 7:32 AM
To: Freesurfer support list 
Cc: Andrew Beaudin 
Subject: RE: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean 
Error

[△EXTERNAL]

Hi Andrew,

Can you send us some data to debug? The link has expired. Also, the command 
line that you are having trouble with.

Thanks.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Andrew Beaudin
Sent: Wednesday, June 29, 2022 10:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error


External Email - Use Caution
Hello Freesurfer Community,
  I am trying to use mri_robust_template (with its default 6 DOF registration) 
outside of the Freesurfer longitudinal pipeline to generate within-participant 
T1 templates from 2 time points.  Unfortunately, I am coming up against a 
'MyMatrix::RotationMean input(s) not rotation' error on images acquired on our 
GE 3T Discovery 750 system, but not our colleagues' Seimens 3T Prisma images.  
I have pasted the output from the --debug flag below (and attached as text file 
- line 188 is the MyMatrix message).   If helpful, images can be download from 
the following link: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/15jKivBPGuiIgzDk9U3fdenEjYAzvpM8z1gjSuYI9TbA6LHUwfOwbvVm65-DjSCqWjMCkWyJFTNIaQ7LKC6u2eC4c4ar3SpKKFcVGTLDzQBqTuxstngHtYy-l0nj6S-UaciytceRn2u4NQfqsV0qU20belkAGT3hGf15PoQzH1qyct_xi_jrBcbkfqjIDrm2NwIbP-ECAml2nRs7dlw7oUJ1oBwNOSZWhBU1HJtR2rOQ-OXAILkt_fJbCZa4BfObRaj2EHelZLhWgkFcgOMQ9SrQZyQ-H0LZ4hoYekPlm8M9iOp76dVNNfEzEx-VTQbED-b4TvGMuavH6dOPqtfkdE5ygdml7xIpFC5vQKVawu9E/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ%3Fe%3DlcovfR

Briefly:
   - the images are skull-stripped niftis and I am running Freesurfer 6.0 
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) on a WSL2 Ubuntu 
18.04 installation.
   - the call is: mri_robust_template --mov 2001A_T1o_brain.nii.gz 
2001B_T1o_brain.nii.mgz --lta 2001A2template.lta 2001B2template.lta --average 1 
--template 2001_template.nii.gz --satit

   -  I have tried the following with no success:
1) using the --iscale flag - same result as shown below.
2) using --inittp 0 - results in a 'Segmentation fault'
3) using --average 0 - same result as shown below
4)

Re: [Freesurfer] recon-all failing to generate wm surface

2022-11-28 Thread Huang, Yujing 
Hi Christopher,

I noticed that you were only running 'recon-all -autorecon1 -autorecon2'. I 
don't think ?h.white surface are generated for the command combinations. 
'recon-all -all' will run all recon steps and generate ?h.white.

Here is a description of recon-all process and flags:
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Christopher Mcnorgan
Sent: Wednesday, November 23, 2022 5:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all failing to generate wm surface


External Email - Use Caution
A student and I have independently been trying to reconstruct a dataset. We've 
tried it a couple different ways using either an additional FLAIR or a T2 image 
and always hit a point where the process halts because of a missing surface 
file:

Loading lh.white surf
error: No such file or directory
error: MRISread(/home/cpmcnorg/VMP/FS_002/surf/lh.white): could not open file

This has happened when running just the autorecon1 step or both autorecon1 and 
autorecon2. I'm using freesurfer 7.2.0 on a linux computer, and my student is 
running 7.3.2 on a Mac. In my most recent test, I ran
recon-all -autorecon1 -autorecon2 -i  -T2  
-subjid 
and I have several surface files (e.g., ?h.orig and even ?h.white.preaparc) but 
not the ?h.white surface. I'm unclear what's causing the recon-all script to 
look for the wm surface before it's been created.
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[Freesurfer] time-series from Yeo's Network components

2022-11-28 Thread stdp82 
External Email - Use Caution

Hi list,

I  would extract the rs-fMRI time-series from spitted components of Yeo's 7 
Network Atlas (fsaverage5).

To this aim, I'm planning to convert the "fmcpr.odd.sm0.fsaverage.lh.nii.gz" 
(obtained by preproc-sess) on fsaverage5.

However, the fmcpr.odd.sm0.fsaverage.lh.nii.gz should still include some 
nuisance variables (CSF, the white matter, motion, first 4 time points).

To address this issue, is it corrected to apply the command lines reported 
below?

mkanalysis-sess -analysis fc.noseed.surf.lh -surface fsaverage lh -fwhm 0 
-notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg 
-fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten

mkanalysis-sess -analysis fc.noseed.surf.rh -surface fsaverage rh -fwhm 0 
-notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg 
-fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten

selxavg3-sess -s subj_folder_name -a fc.noseed.surf.lh -overwrite -no-con-ok 

selxavg3-sess -s subj_folder_name -a fc.noseed.surf.rh -overwrite -no-con-ok




Thanks

Stefano


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[Freesurfer] Creating or Using Alt Templates

2022-11-28 Thread Olivier Brown 
External Email - Use Caution

Dear Freesurfer experts,

I am using a pediatric sample for my study. I understand that the default 
template has been used with younger samples in the past. However, is there a 
command or flag to input an external template, such as the MNI? Otherwise, is 
there a method for creating my own template using the acquired imaged with 
Freesurfer? I cannot seem to find many resources online for selecting alternate 
templates in the preprocessing steps of recon-all.

Warm regards,
Olivier Brown
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[Freesurfer] FS_7_2_0_Ubuntu_18_04_06.ova.7z password

2022-11-28 Thread Marcel Heers 
External Email - Use Caution

Can you please share the password for the above mentioned VirtualBox with
me?

Thanks in advance!
Marcel
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[Freesurfer] Permission denied error

2022-11-28 Thread Adam Tartaglia 
External Email - Use Caution

Hello,

Immediately after running recon-all, I get an error that says cannot create
directory, permission denied. I am not sure as to why this is happening. My
license is in the correct location.

Thank you for your time,

- Adam
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