Freesurfer

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30084 discussions

Confusion about mean CT measures after registration
by Dongyue Zhou 08 Oct '21

08 Oct '21

External Email - Use Caution Dear FreeSurfer experts: I use the command recon-all qcache to get filesub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file. I want to know mean CT measures of every ROI after registraion in one subject. And I know mean CT is calculated by dividing CT of all vertices by the number of vertices. Can I use fsaverage/label/?.annot as atlas to calculate mean cortical thickness of every ROI directly? Or should I transfer sub_01/label/?.annot to fsaverage ?

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Thalamus-proper gone?
by Cubillo, Ana 08 Oct '21

08 Oct '21

External Email - Use Caution Dear Freesurfer community, I am using the freesurfer version through a singularity container (https://secure-web.cisco.com/1j_Zv2QItcuWtdQRfU3BocTH20Tz0V5FYnvMZKQNUHVHrS…) in a HPC cluster. It all ent well until I extracted the subcortical regions, where I see that for all of my subjects the values of Thalamus-proper are 0. When I look further into it, I see that my FreeSurferColorLUT.txt file only includes Thalamus but not Thalamus-proper. I found this thread which mentions that the thalamus-proper was removed from recent FreeSurfer versions: https://secure-web.cisco.com/1_BT-tajm4M7yDBVb5BfWwjdB0iHk_Liz1vM5WOL3zLziL… Unfortunately, when I try to look for information online on whether they are exactly the same or whether they differ, I only found the FreeSurfer wiki page about the FreeSurferColorLUT<https://secure-web.cisco.com/1i1A_DRuhjTo1dIQFd0ggAD58K_mWkVlkDzs4I3ydFj4x2…>(i.e., look up table) which includes this note: “* Thalamus-Proper is the correct segmentation for the Thalamus.” But this is a page from 2015 so might not be up to date anymore. In this thread<https://secure-web.cisco.com/1IMfKsWyLM9gWH6vW81VZUrGlkiDnwKUtLgzVagH0ZHERn…> from 2017it was also discussed that the thalamus-proper is the correct one but it is also stated that name should be changed, so maybe they have done this now. Basically - do I need to re-run the recon-all with a different freesurfer version to extract Thalamus-proper or has this been replaced by Thalamus now? Thanks!! A

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Confusion Working with Longitudinal and Group Analysis Tutorials
by Giuseppe Miranda 08 Oct '21

08 Oct '21

External Email - Use Caution Hello, I have been looking through tutorials on the website and referencing the freesurfer mail archives, but I am a bit unsure if I am following the correct procedures for my analysis. The main source of confusion on my end stems from trying to apply tutorials (and in some cases the tutorials they reference) to my longitudinal data. I appreciate your help in advance. I have longitudinal data with scans from two time points. My variables were all collected at time point 1 (TP1). I am interested in change in cortical thickness in relation to these variables as well as interacting effects on cortical thickness; some of these variables are continuous (e.g. suvr) and some are categorical (e.g. alleles). My initial goal was to use QDEC, but I quickly learned that should use glmfit. For the purpose of understanding, I am writing in focusing on age and suvr as my variables. I started with the longitudinal tutorial. 1.) The first point of confusion came near the end of the tutorial at "long_stats_slopes". The command runs for me, but I'd appreciate a second look on whether this is correct: long_stats_slopes --qdec $SUBJECTS_DIR/long.qdec.table.dat --stats lh.aparc.stats --meas thickness --sd $SUBJECTS_DIR --do-avg --do-rate --do-pc1 --do-spc --do-stack --time years --stack-avg [desired path]/stack-avg --stack-rate [desired path]/stack-rate --stack-pc1 [desired path]/stack-pc1 --stack-spc [desired path]/stack-spc >From there, the tutorial says to run my data through the glm tutorial. I have several points of confusion here - the first being that I'm concerned that I may not have my data set up correctly. 2.) I looked at the FSGD examples and built my file from them, and I also referenced the mail archives for similar projects to mine. I am unsure as to whether I should be using the [LONG] files created or the [BASE] files created with the longitudinal tutorial in my FSGD file. For example, if I am just looking at age and another factor (suvr) should my FSGD look like this... GroupDescriptorFile 1 MeasurementName thickness Class subject Variables age suvr Input Subject1_TP1 subject 57 0.93 Input Subject1_TP2 subject 57 0.93 Input Subject2_TP1 subject 64 1.22 Input Subject2_TP2 subject 57 1.22 Or should it point to the directories made during the [BASE] step of the longitudinal tutorial like this? GroupDescriptorFile 1 MeasurementName thickness Class subject Variables age suvr Input Subject1_base subject 57 0.93 Input Subject2_base subject 56 1.06 3.) From there, I understand that I need an individual contrast matrix for each contrast that I'd like to run. Here is what I have been using: Age: 0 1 0 Suvr: 0 0 1 Age x Suvr: 0 1 -1 4.) Next, I ran through the rest of the GLM tutorial to assemble the data and run glmfit, followed by a clusterwise comparison for multiple comparisons mris_preproc --fsgd file_name.fsgd \ --target fsaverage \ --hemi lh \ --meas thickness \ --out lh.file_name.thickness.00.mgh mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.file_name.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.file_name.thickness.10.mgh mri_glmfit \ --y lh.file_name.10.mgh \ --fsgd file_name.fsgd dods\ --C age.mtx \ --C suvr.mtx \ --C age_suvr.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.directory_name.glmdir mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces 5.) My last question is, if I want to run glmfit to analyze my data with other variables, is there anything that I have to delete or re-run on my end? From what I understand, I would only have to run glmfit and its' corrections again. I appreciate your help - I just want to make sure that I am, and that I am following these tutorials properly. Vince

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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

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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

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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

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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

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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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