Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

number of seeds in fcseedcor
by Nasiriavanaki, Zahra,M.D. 08 Oct '21

08 Oct '21

Hi Freesurfer experts, I was wondering how many seeds we can use in fcseedcor command? I have more than 100 seeds and when I use all those seeds in the below command, I get this error: Command: fcseedcor -s $subj -fsd rest -seed 1.dat -seed 2.dat -xreg global.waveform.dat 1 -xreg vcsf_mean.dat 1 -xreg wm_mean.dat 1 -xreg mcprextreg 6 -hpf .01 -lpf 0 -nskip 0 -sim 1000 -o cor_all.dat Error: Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.768795e-22. > In ^COperation terminated by user during fast_glmfit (line 35) Appreciate your help, Mona Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

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A question regarding a Freeview command
by inbal paran 08 Oct '21

08 Oct '21

External Email - Use Caution Dear FreeSurfer developers, I am trying to run a group analysis to test for an association between *gray matter volume* and a behavioral measure of interest. reacon-all ran OK for all my subjects as well as mris_preproc followed by mri_surf2surf, and finally glmfit. Finally, I wanted to visualize the significant voxels using freeview and followed the command line in the tutorial of the group analysis ( https://secure-web.cisco.com/1_d3qazq-_19W6y1XEkeVPINXH5vgktFtuM1FrpU_HJNr4…) However, since I am talking about volume and not surface, I wasn't sure how to edit the final command to visualize my results in freeview. I want to make sure it will include significant voxels both in subcortical + cortical regions. Should I use a stats.table file as an input? As you probably understand, working with Linux and FreeSurfer are both very new to me, if it's possible, any help would be greatly appreciated. If it's relevant, these are the details of the version and platform I'm using: 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) Platform: Ubuntu 20.04.1 LTS 3) uname -a: Linux inbal-paran 5.11.0-37-generic #41~20.04.2-Ubuntu SMP Fri Sep 24 09:06:38 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) I also attached the mris_preproc log files in case it can help Kind regards, Inbal Paran -- *Inbal Paran, M.PT <http://secure-web.cisco.com/1TCV1fAKzZJ5GOMgMi06jDdgf5mlDmrjtvqzBaNtTAOycuW…>.* Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy Department, Recanati School for Community Health Professions. Faculty of Health Sciences at Ben-Gurion University of the Negev.

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Comparing volumes before and after editing
by Kang, Jee Won 08 Oct '21

08 Oct '21

External Email - Use Caution Hello all, I'm very new to Freesurfer and have started with quality-checking recons. I wanted to know if there is a way to compare volumes before and after edits were made before recon-all has been re-run. For example, if we have brainmask.mgz that has been edited and brainmask_ORIG.mgz before any edits were made, is there a way to create a volume overlay and extract the areas where edits were made (perhaps parsed from aparc+aseg)? Thank you for your assistance on this! -Jee Won

2 1

matlab: command not found - How can I solve this?
by Camila Fernandes da Silva 08 Oct '21

08 Oct '21

External Email - Use Caution Hey, I'm totally new into Freesurfer and I need some help with my Matlab. I tried to do "recon-all -s <.....>/ -lgi But as you can see, It shows an error related to matlab... I tried everything! But nothing is working. I have heard that we should modify the startup.m file... But, what am I supposed to do with it? I'm using the Freesurfer 7.1.0 version ----------------------------------------------------------------------- #@# Local Gyrification Index lh Fri Oct 1 15:25:01 EDT 2021 mris_compute_lgi --i lh.pial *matlab: Command not found.matlab5: Command not found.* ERROR: *Matlab is required to run mris_compute_lgi!* Command exited with non-zero status 1 @#@FSTIME 2021:10:01:15:25:01 mris_compute_lgi N 2 e 0.01 S 0.00 U 0.01 P 94% M 2784 F 0 R 736 W 0 c 11 w 15 I 0 O 0 L 0.05 0.12 0.10 @#@FSLOADPOST 2021:10:01:15:25:01 mris_compute_lgi N 2 0.05 0.12 0.10 Linux developer-VirtualBox 5.4.0-87-generic #98~18.04.1-Ubuntu SMP Wed Sep 22 10:45:04 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s controle01_T1 exited with ERRORS at Fri Oct 1 15:25:01 EDT 2021 For more details, see the log file /home/developer/freesurfer/controle01_T1/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1cisSzDB61L2V_wjkzh5VutTxw6cDnzHhZoLYWlTI2KVRLa… -- Atenciosamente, Camila Fernandes Licenciatura em Física - IFUSP

2 1

Brodmann areas volumetric parcellation freesurfer 6.0
by Ahmed Radwan 08 Oct '21

08 Oct '21

External Email - Use Caution Dear FreeSurfer experts, I would like to generate .mgz Brodmann parcellation maps in FreeSurfer 6.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) to be precise. Is this possible? I found this thread (https://secure-web.cisco.com/177FKNV88nkCNrwgn4jIC93-E_ZjHSBW0BXiH1uX3pOj28…) asking a similar question but aiming to propagate those parcellations into WM using FS 7.1. Thanks in advance, Ahmed Radwan

2 1

Repeated measures analysis
by Abbie Taing 08 Oct '21

08 Oct '21

External Email - Use Caution Hi all, I have a between subjects factor (3 groups) and within subjects factor (3 stimuli type). I am interested in comparing cortical volume differences between groups and stimuli (i.e. group x stimulus interaction). What pipeline can I use to examine this? Many thanks, Abbie

2 1

SAMSEG output orientation not the same as input images
by daedalus39＠aol.com 08 Oct '21

08 Oct '21

External Email - Use Caution We have recently installed FS-7.1 and have tested a few “ADNI” images with SAMSEG. The process runs to completion, but the output (seg.mgz) appears upside-down and rotated about 90 about the X-axis. We are passing seg.mgz through BrainStorm to create NiFTI images. We do not believe that this is a BrainStorm issue inasmuch as the same images run through recon-all (fully separate proc) yield output images in the same orientation as the original images. I found a thread from 2012 with a similar output orientation issue, but the I did not see a response that resolved this. Any solution or insight would be greatly appreciated Sincerely,Randolph Andrews (PS. listserv item from 2012)Re: [Freesurfer] integrating FSL and FreesurferChris Filo Gorgolewski Tue, 09 Oct 2012 01:03:57 -0700https://http://secure-web.cisco.com/1bJm-kJVNOrTUaWjoqVk32d_m43kHXTpDrk8lcY-0m9IZL70ouR0Amj-rARrWUqpHqs37bd05gpqsZ5ysfX2IwhyEvB-jtySLbpgfVIwI9odls_4K82Kvhw3QUndLV0gJI7R_qOETwN5R8IsMiDFIovreM-3E6uNLDr9ua3ZEczUFu9zQt9L__yWHK3owmBE4NgW7-Jnn33sNGKV7QlzDb88gcre-4JwPKkrKdRylwImRU0aoDyCaRRFgoCRV_0jNFU_SZCrwzKcpPOyFWMzFRA/http%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg24896.html

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non-brain tissue segmentation from T1-w images
by Banik, Rana 08 Oct '21

08 Oct '21

External Email - Use Caution Hello All, I am a beginner in freesurfer. Was looking for resources to perform volumetric segmentation(not surface mesh) for non-brain tissues like Muscle-skin, fat from T1-w MR images. Is that feature available in freesurfer? I have used FSL for WM, GM, CSF segmentation. Also looking to protect the inter-subject variability without registering the head volumes to MNI or another atlas. -Rana

2 1

Running -localGI without Matlab
by Soichi Hayashi 07 Oct '21

07 Oct '21

External Email - Use Caution Hello. I am trying to run recon-all with -localGI option. I am running freesurfer on HPC clusters where there is no Matlab license. When I add this option, freesurfer fails with this error message. mris_compute_lgi --i rh.pial ERROR: Matlab is required to run mris_compute_lgi! I am running freesurfer where it has access to MCR runtime to run compiled Matlab script. Is it possible to compile whatever the Matlab script that this module is using so that it can run without the full Matlab installation/license on our HPC systems? Thank you! Soichi

1 0

Re: [Freesurfer] Password
by fsbuild 07 Oct '21

07 Oct '21

External Email - Use Caution Sending the info to your email address shortly. - R. On Oct 6, 2021, at 22:25, Francisco Polito haro <galfox83(a)hotmail.com> wrote:        External Email - Use Caution                External Email - Use Caution        Dear Freesurfer team, Could you provide me the password for the user 'developer' of the VM Freesurfer installation? Many thanks in advance, Best regards,Francisco Polito, LFA_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1KoZLY6VF10O_YMbs6-9VcK_BEU35SGNNv7OYVZx9BP6Zssr1q5BjsZ8KQVvRnRwRs3gcMn4vNTnu0w9avJv7LT3wL9cEqx6rVgIr4dtoZPvkgY8ClahAzWfN0mbk2Wi2cWgSaSFNM2RaZ8bSxJczJQb_9u-CT_eApU1Ah2qCG5dqh4kB5PAqusBzMzNnsEq8zltg22WFILdiOHxSVQR-xBYr5QQJnl6f5dhHG5ikG5V_UFpi0e2RiuYifD-yytu8AYda7grkiDHDsFDTYSXifg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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