Re: [Freesurfer] Sourcing freesurfer

2023-06-01 Thread fsbuild 
External Email - Use Caution


Hello Pedro,

  

It does not look like you are using a standard installation of freesurfer given 
the path you list below as /root/freesurfer.

  

We have information available about how to use either WSL (Windows 
Subsystem for Linux) to host Ubuntu Linux in order to run Freesurfer on 
Windows, 
https://secure-web.cisco.com/1kqIIthfElwIFp4xfRtH02uxDl8MR86sRRP-ugqp0vSmGTwouZW4HNNYu-ASZ16mZ_Iuv0ijLc4n8GoJ-PYDNxXI8iR65z66fu0iMaWl3Q4GI04QRmhW1E1VKfT4SUVJ1fRILMGimNKa_5j_d0AGmhmmSni2m3muR4VtH0r1zcBiDu49VloKQOXl9Awx2k_HbUvDp56pSAZg9124Enh_wkkmkFeY9NYPTbyA0lowGERTcQ7UhRL6hsAWs0tf6YnnF8IFHbQ3jYyUJ_lLUSlYTBlZJErEeTTmQJGVZGIoS0Uba_5dinxPiH14LzwuuzJhfpjfqvDuc8hPmKTrKQHlAOw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl
 - or you can 
install VirtualBox on your Windows machine to run a VM we provide for download 
with freesurfer 
already installed and setup to run (see 
https://secure-web.cisco.com/1v32HavIAAMjouxecLl5yEhLk0tyE2hxIHnDGZC-o-FlJlsmrLmxezyaPUZwi0vEC-0ScvlOmdUUtn8wqQD3Pmb0jjoVLpjoElqsQkvGsJbqSqvzzVi4Mdqjwx6p3OWVg1QXTtBPYg201z5NbJXNM8GlniMfK37qtSsIZmObLTiLC8XaozODnZK7BLJvIelNxvGdmZwKIScPZfwOKmOeo98rG_33IJjzuYEYdhHYOTohWJTAS5D5d7uVgWo4_0KZKpYO-4oQ7PlXaEPIiCHxZ8-XKD5KJNQYP2BwMArrVh-d8bEy4hpQVnFbnRKLPkywym_Vdwsd8hZZSZjWh_RSRHA/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FVM_67)

  


For WSL, once you have Ubuntu Linux running, we recommend using one of 
the debian (.deb) package installers listed on the Freesurfer 7 download
 page that matches your Ubuntu system 
(https://secure-web.cisco.com/1q0Hyt7h01b-vvXLm4oWRsX0bWB4JcKCG1QCz9R_lYE6XHQort-mLk13RKkWZGUGVILN93q8rOKfcVjK2UIYfo_9T-OlnHE9o_O90iMChssl7wBoxAVUd71MYUOp2XHPMRpUCQtlg2dE_CPOa-v_VTRECYiAzYRNZUet678R2gYy5Sww1akjBHBEZBTgW1NpqtHCmWOa2TUozHaFqV6Z3bspTOygx_71HpaMkLMbpiFZG96mCGqJjBK0_yKw8UMUr0gr3i0RvxPMty4cn6tt0jakn4uea25db9BQmYAp2g3MYhVG3_XCzfZ-AjTEBNBNcorpywfrrxPzn-zIxNn99Zw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads).
 So for 
Ubuntu 22 running in WSL, you would download one of the 
freesurfer_ubuntu22-7.X.X_amd64.deb files into Ubuntu linux and install 
it. That would install freesurfer as /usr/local/freesurfer/7.x.x in the
 Ubuntu Linux image running in WSL. In the VM, freesurfer 
7.2.0 is 
already installed as /usr/local/freesurfer/7.2.0



We recommend you verify you are using (or try) one of the setups above.


  

- R.

  


On 6/1/23 11:38, Pedro henrique barradas (phbarra...@hotmail.com) wrote:






  External Email - Use 
Caution

  

Hello!

I'm having a couple problems with the final installation steps





When I attempt to export $FREESURFER_HOME=$HOME/freesurfer it tells me:

bash: export: ´#HOME/freesurfer=root/freesurfer`: not a valid identifier


When I source it, it now says it cannot find the directory

and gives back the following answers:

bash: /root/freesurfer/SetUpFreeSurfer.sh: No such file or directory
I also tried doing "sourceSetUpFreeSurfer.sh"
 from the freesurfer directory and I got this response:

bash: /root/freesurfer/FreeSurferEnv.sh: No
 such file or directory






Also,

When I typeecho $FREESURFER_HOME I get

root/freesurfer




But when I type pwd $FREESURFER_HOME it gives me
  

  
c/mnt/Users/ASUS/Downloads/freesurfer

  

  




  
I greatly appreciate any advice. Thank you

  
Best wishes

  







  

  
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[Freesurfer] [FreeSurfer] SyntSR for noise reduction and/or cross-scanner comparisons

2023-06-01 Thread Linnman, Clas,Ph.D. 
External Email - Use Caution

Hi FreeSurfers

We are looking at cortical thickness after spinal cord injury in a pooled 
sample from three sites. All have 1x1x1 mm T1. Our current approach has been to 
exclude noisy data (16/159 participants), and to account for scanner 
differences using site as dummy variables.

We are considering using SynthSR  for two purposes:

  1.  reduce motion artefacts in (some) scans
  2.  better merge data between different scanner sites

If using SynthSR for noise reduction seems like a good idea, is it best to then 
run SynthSR on ALL datasets for consistency?


Best
Clas Linnman





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Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3

2023-06-01 Thread Huang, Yujing 
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Hi Annchen,

Your cp commands are missing destination file operands, see the errors in 
recon-all.log.

ln -s $FREESURFER_HOME/subjects/fsaverage and ln -s 
$FREESURFER_HOME/subjects/${hemi}.EC_average create symbolic links to 
directory. You will have to copy those two directories for your subject. I 
think if you copy them before recon-all, it won’t go through the codes to 
create the link.

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Annchen Knodt
Sent: Thursday, June 1, 2023 2:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3


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Hello,

I'm trying to run freesurfer v5.3 recon-all and running into an error I'm not 
sure how to troubleshoot.  I'm using essentially the same commands that i've 
successfully used to run version 6.0 recently, and that i've also successfully 
run 5.3 with in the past.

On my first pass, I attempted to run this full recon-all command:

/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink 
-all -s sub-0223_mprage -openmp 1 -i 
/cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz

And eventually got the error:

  MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): 
could not open file

Lots of lh surf files were produced as well as 3 of the lh stats files (aparc, 
curv, w-g), but nothing for rh, and I could not find the rh.white file.  I then 
tried running rh using:

/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink 
-all -s sub-0223_mprage -openmp 1 -hemi rh

And eventually got the error:

  
MRISread(/work/long/freesurfer_v5.3_DBIS/rh.EC_average/surf/rh.sphere.reg): 
could not open file

One thing that seems weird about the second error is that it is looking in 
$SUBJECTS_DIR instead of $SUBJECTS_DIR/ for the rh.sphere file, when 
the file does exist in $SUBJECTS_DIR//surf (but not the top dir where 
it's looking)

Also wanted to note that i'm running this a slightly tweaked version to remove 
symlinks which aren't allowed on the cluster i'm working on (which is running 
CentOS 8):

$ diff 
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink 
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all
3447c3447
<   cp $subj1 ${diffsubj}_tmp
---
>   ln -s $subj1 ${diffsubj}_tmp
3753c3753
< cp $subj1 ${diffsubj}_tmp
---
> ln -s $subj1 ${diffsubj}_tmp
3911c3911
< set cmd=(cp $FREESURFER_HOME/subjects/fsaverage)
---
> set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4028c4028
<   set cmd=(cp $FREESURFER_HOME/subjects/fsaverage)
---
>   set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4157c4157
<   set cmd=(cp $FREESURFER_HOME/subjects/${hemi}.EC_average)
---
>   set cmd=(ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average)

Any tips on how I can troubleshoot this?  Attaching recon-all.log file.  
Thanks!!

Annchen



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[Freesurfer] Error with running retinotopy glm

2023-06-01 Thread Loïc Daumail 
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Dear FreeSurfer experts,

I am trying to perform a retinotopy analysis using fs-fast with Freesurfer
version 7.3.2 on a Mac OS Monterey Version 12.6.2

Here is the error I am having (I saw this same error in the archive, but I
wasn't able to find any solution email that followed regarding this issue):

Saving X matrix to
/Users/tong_processor/Desktop/Loic/retinotopy/old_Hojin_mri_data/F094_fsfast/sess01/bold/retinotopy.F094.07.lh/pr007/Xtmp.mat
Error using svd
Input to SVD must not contain NaN or Inf.Error in cond (line 35)
  s = svd(A);Error in fast_selxavg3b (line 389)
 XCond = cond(XtX);Error in sxa3 (line 9)
fast_selxavg3b('/Users/tong_processor/Desktop/Loic/retinotopy/old_Hojin_mri_data/F094_fsfast/sess01/bold/retinotopy.F094.07.lh/sxa3.config.txt')Error
in run (line 91)
evalin('caller', strcat(script, ';'));

Please see attached the code I used, and the associated files of the
analysis

Thanks in advance for your help!
Best,
-Loïc
PhD candidate
Vanderbilt University
<>
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[Freesurfer] Sourcing freesurfer

2023-06-01 Thread Pedro henrique barradas 
External Email - Use Caution

Hello!
I'm having a couple problems with the final installation steps

When I attempt to export $FREESURFER_HOME=$HOME/freesurfer it tells me:

  *   bash: export: ´#HOME/freesurfer=root/freesurfer`: not a valid identifier

When I source it, it now says it cannot find the directory
and gives back the following answers:

  *   bash: /root/freesurfer/SetUpFreeSurfer.sh: No such file or directory

I also tried doing "source SetUpFreeSurfer.sh" from the freesurfer directory 
and I got this response:

  *   bash: /root/freesurfer/FreeSurferEnv.sh: No such file or directory

Also,
When I type echo $FREESURFER_HOME I get
root/freesurfer

But when I type pwd $FREESURFER_HOME it gives me
c/mnt/Users/ASUS/Downloads/freesurfer

I greatly appreciate any advice. Thank you
Best wishes

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Re: [Freesurfer] Problem installing FreeSurfer

2023-06-01 Thread Michelangelo Fabbrizzi 
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Dear all,

thanks for your reply. I did as below and the first time I run the command 
“freeview”, it works. Then if I try to open it again, it gives the same error 
as below…can you help me please?

Thanks, appreciated,

Michelangelo

> Il giorno 31 mag 2023, alle ore 23:43, fsbuild  ha 
> scritto:
> 
> 
> Please make sure you have downloaded a freesurfer license.txt file by filling 
> out the form at,
> https://secure-web.cisco.com/1hc5Xc7px__3EjuoO1_Ni4orsJzMv2R3iM-TJ3g17W6pD1Jv2-zP7lu8luJ73VfXWqrsbHX_7eZc4dqW0qWuk88NFuUNQxZ7E35P7PaGZrx3_HXCb5RW8jZWDDtzYCB_ukWSy3Fz5lbERnNvMc0l8SgVPh66EIA3pkAdAz9x6wHNX_sxP2xYQ4KCLPgHYRndbQ5stn4tNAVOQ7iNJMa_86RhGR2kP6sEXQ_MQzPRxYuQdUq-PQnSOzmYT1KnKZFMtzRCEAgwtXdhwDvUybAWLzyl6qjmND8kf0yQveUBT1m0eM_PHPXIOqS9cs64lCoxG/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
>  
> 
> 
> Place the license.txt file you will receive in your home directory, e.g., 
> 
> $ cd $HOME
> $ head -1 license.txt
> 
> 
> Set the FS_LICENSE environment variable manually (and/or in your shell 
> initialization file, e.g., .bashrc) to point to the license file,
> … here set from a terminal window running bash shell ...
> 
> $ export FS_LICENSE=$HOME/license.txt
> 
> Setup the freesurfer environment,
> 
> $ export FREESURFER_HOME=/Applications/freesurfer/7.4.0
> $ source $FREESURFER_HOME/SetUpFreeSurfer.sh
>  freesurfer-darwin-macOS-7.4.0-20230504-55dcf98 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer/7.4.0
> FSFAST_HOME   /Applications/freesurfer/7.4.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/7.4.0/subjects
> MNI_DIR   /Applications/freesurfer/7.4.0/mni
> 
> $ which freeview
> /Applications/freesurfer/7.4.0/bin/freeview
> 
> Then try running freeview with no arguments to see if it brings up an empty 
> window,
> 
> $ freeview
> 
> If that works, quit freeview and try running it again with an example volume 
> included in the distribution,
> 
> $ freeview  $SUBJECTS_DIR/bert/mri/brain.mgz
> 
> If that works, quit freeview and try your own surface/volume files.
> 
> - R.
> 
>> On May 31, 2023, at 17:05, Michelangelo Fabbrizzi  
>> wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> Dear Sirs,
>> 
>> I am new to Freesurfer. I installed as shown on website and added the 
>> license.txt, however when I open freeview I get an error 
>> "/Applications/freesurfer/7.4.0/bin/freeview: riga 2:  2047 Segmentation 
>> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“”
>> Attached the report.
>> 
>> Freesurfer version: freesurfer-darwin-macOS-7.4.0-20230510-e558e6e
>> Platform: MacOS12.6.6
>> Mac: Macbook Pro Intel Core i5 dual-core
>> XQuartz2.8.15
>> XQuartz2.8.5
>> Can you help me please?
>> 
>> Thanks!
>> 
>> Michelangelo
>> 
> 
> 

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[Freesurfer] pass code

2023-06-01 Thread Agosti, Giulia 
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Hello,

I am following the instruction from this page: freesurfer@nmr.mgh.harvard.edu 
and a pass code is needed for this 7z archieve. Could you send me the pass code?

Kind regards
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