Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

mri_sclimbic_seg: --conform not conforming?
by Markus Handal Sneve 26 Sep '22

26 Sep '22

External Email - Use Caution Hi, I’m testing mri_sclimbic_seg in the new FS version (7.3.2). My structurals are 0.8mm isotropic, so I’m adding the —conform flag, but still get this error: [cid:6758653C-0371-4C06-8D50-100648474ED0] Any ideas? And, BTW, I had to set the environmental variable HDF_USE_FILE_LOCKING to FALSE to get the tool running. Perhaps a tip to add to the wiki, if not people can now see it here. Thanks for your great work! Cheers, Markus Markus Handal Sneve, Ph.D. Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo

3 4

Re: [Freesurfer] segment_subregions failed
by Markus Handal Sneve 26 Sep '22

26 Sep '22

External Email - Use Caution Hi, Sorry if this ends up in the wrong place, had to reactivate my FS-mailing list account. So I get the exact same error as reported by Mamun Al-Amin when running segment_subregion (FS v7.3.2). Fresh terminal, no other FS version running in the background, build-stamp.txt shows the correct version. Hopefully you can see the screenshot below, sadly cannot ctrl-c text out of our cluster [cid:02AE0EFB-80BC-4895-B44D-AC05CB77D890] Thanks! Markus Handal Sneve, Ph.D. Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo

2 4

Tracula statistics outputs
by King-Wai Chu 26 Sep '22

26 Sep '22

External Email - Use Caution Hi, I have 3 questions on tracula statistics outputs. 1) There are duplicate points in pathstats.byvoxel.txt, is it normal? I didn't try it on all 42 tractcs. For the few I've looked at, they all have duplicate points. I used the default setting in the config file to run trac-all. 2) When I do along-tract statistical analysis, sig.mgh and z.mgh are 1D files. When embed the sig.mgh and z.mgh statistical maps from the analysis into the template .trk (*.display.trk, which is 3D), it seems to me that sig.mgh and z.mgh don't have enough information to give *.display.trk the voxel values for the *.overlay.trk. There is no one-to-one voxel corresponding between sig.mgh and *.display.trk. What am I missing? Or what's the embedding process do? 3) When I convert .trk(*.overlay.trk, for example) to nii.gz or ascii using dmri_trk2trk or mri_convert the voxel values of the .trk file don't get converted into the .nii.gz or ascii file, only the x,y,z coordinates are converted. Is there a way to get the voxels values of the .trk file when converting to .nii.gz or ascii format? Thanks, King-Wai -- King-Wai Chu, Ph.D. Program Analyst Mental Illness Research, Education and Clinical Center (MIRECC, VISN3) James J. Peters Dept. of Veterans Administration Medical Center (OOMH) 130 W. Kingsbridge Road Bronx, NY 10468

1 0

intrareg: Undefined variable
by miracle ozzoude 26 Sep '22

26 Sep '22

External Email - Use Caution Hello, I am trying to run TRACULA using FreeSurfer version7.2. I followed the instructions on the tutorial website for cross-sectional study with 1 scan (see link below). However, I keep getting "intrareg:Undefined variable" error whenever I run the first step "trac-all -prep -c tracula.file". I checked my config file and I did set intrareg = 3. Any suggestions on what the issue is/how to fix it? I have attached my config file in the email below, in addition to the log file. The participants' recon-all were processed using freesurfer v6.0 Many thanks, Paul

1 1

confirmation of processes/commands used in full processing pipeline
by Harriott, Emily M 26 Sep '22

26 Sep '22

External Email - Use Caution Dear FreeSurfer experts, I hope this email finds you all doing well. I'm a second-year doctoral student (and beginner FreeSurfer user) trying to use FreeSurfer to segment gray and white matter in 90 T1 images of children/adolescents (with reading disorders, Neurofibromatosis type 1, and typically developing) for a project; I have two questions about processing these images, and I would be so very grateful to receive some thoughts/suggestions/advice etc. from some FreeSurfer experts such as yourselves. I ran recon-all on each of those 90 images, but one single run of recon-all left too much dura in the gray matter segmentation and too much white matter out of the white matter segmentation (the amount of white matter left out varied depending on the intensity contrast of each image). To fix the dura/gray matter issue, I re-ran recon-all using the -gcut flag and edited out by hand the remaining dura; this seemed to help. To fix the white matter issue, I tried adding control points and adding white matter voxels and re-running recon-all; this unfortunately did not seem to help, as control points led to worse segmentation and the added white matter voxels had minimal to no effect. So, after some experimentation, I have created a full processing pipeline to use on my data. But, before I apply it to all 90 images, I wanted to confirm with you all experts that this will 1) work and 2) do what I want it to do. Question 1: If I process my data in FS 7.2.0, can I go back and analyze it using QDEC in FS 6.0.0? Or do I have to process it in 6.0.0 to use QDEC? Question 2: Here is my pipeline (see below). Will this work? Will it do what I want it to do? Do you have any suggestions? I'm a beginner; is there anything I should be careful of or watch out for that I don't know about? After some experimentation on a subsample, this pipeline appears to work, but I really want to ensure it is doing what I want it to do and will do that consistently. For one subject.... I first run the initial recon-all (with some flags). $recon-all -i <input image> -s <subjID> -sd <subjects_dir> -wsthresh 10 -gcut -qcache Next, I open brainmask.mgz in FreeView and edit out the remaining dura mater by hand. When I save this new brainmask.mgz, I overwrite the old brainmask.mgz with this new edited brainmask.mgz. I then run multiple second iterations of recon-all, allowing me to use different seg-wlo thresholds (seg-wlo thresholds of 40, 50, 60, 70, 80, 90 are applied to each image). The multiple second iterations of recon-all are: $recon-all autorecon2 -s <subjID> -sd <subjects_90> -seg-wlo 90 -qcache $recon-all autorecon2 -s <subjID> -sd <subjects_80> -seg-wlo 80 -qcache $recon-all autorecon2 -s <subjID> -sd <subjects_70> -seg-wlo 70 -qcache $recon-all autorecon2 -s <subjID> -sd <subjects_60> -seg-wlo 60 -qcache $recon-all autorecon2 -s <subjID> -sd <subjects_50> -seg-wlo 50 -qcache $recon-all autorecon2 -s <subjID> -sd <subjects_40> -seg-wlo 40 -qcache (Note that I have 6 distinct subjects_?0 folders for 6 distinct seg-wlo values) In FreeView, I then visually assess the image/segmentation produced by each seg-wlo threshold to select the threshold that most optimally segmented the gray and white matter. I save the subject folder with the optimal seg-wlo threshold, as determined visually in FreeView by me, to a new subjects directory; this new subjects directory's folder is specified "SELECT". I now have measures of cortical thickness, surface area, and volume, but I also want measures of local gyrification index (LGI). With MATLAB 2022a active (I'm working on a large computing cluster, so I have to activate MATLAB/2022a as a module), I run the LGI recon-all. $recon-all -s <subjID> -sd <subjects_SELECT> -localGI -qcache I then obtain the measurements of LGI. To run this line, I also have a .bashrc file in my subjects_SELECT folder that has one line: MEASURE1 = pial_lgi. $recon-all -s <subjID> -sd <subjects_SELECT> -measure pial_lgi -qcache Then the data go into QDEC and I should be able to analyze from there. Any confirmations/denials, suggestions, or advice you all have would be so very greatly appreciated. Thank you so very much! Emily Harriott Doctoral Student, Vanderbilt University Nashville, TN

2 2

Fully funded postdoctoral fellowship in Ottawa, Canada
by Lauri Tuominen 26 Sep '22

26 Sep '22

External Email - Use Caution Drs. Lauri Tuominen and Sara Tremblay at the Institute of Mental Health Research in Ottawa are looking for a postdoctoral fellow. The candidate should have strong experimental skills in resting state fMRI to be able to develop and implement an fMRI protocol for targeting TMS in the treatment of major depressive disorder. The Institute of Mental Health Research in Ottawa hosts a Siemens mMR Biograph PET/MRI scanner, state-of-the-art TMS equipment, and excellent computing resources. The selected candidate will gain experience in conducting a randomized controlled trial, an opportunity to explore a range of questions using multimodal data including TMS, fMRI, and PET and have the opportunity to work with a diverse team of experts. For details, please visit: https://secure-web.cisco.com/1pBcLS2FQ9PAJwHQqnBym-wJFvufqJgyeD4wunEKVvgzfr… If you have questions regarding the position please send an email to Lauri Tuominen (lauri.tuominen(a)theroyal.ca)

1 0

SAMSEG - modification of the template files
by Mikolaj Pawlak 25 Sep '22

25 Sep '22

External Email - Use Caution Dear Freesurfers, I have been using samseg for a while and like it a lot. Thank you for this tool. How do you modify the template for this tool? Is there a guideline for this? I would like to divide Fluid_Inside_Eyes label to left and right and improve the bone information in the template. What is the procedure? thanks, Mikolaj Pawlak

2 7

Sclimbic segmentation error
by bar gen 25 Sep '22

25 Sep '22

External Email - Use Caution Hi all, I am receiving this error when trying to run sclimbic module. mri_sclimbic_seg --i /Users/mdbargen/Documents/control-T1 --o /Users/mdbargen/Documents/control-limbic --conform Segmenting image 1/68 Loaded input image from /Users/barisgenc/Documents/Kontrol-T1/Acar_Ebru-T1.nii.gz Traceback (most recent call last): File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 1048, in <module> main() File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 312, in main segmenter.process_files(**params) File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 577, in process_files post, seg, vox_counts, volumes, mean_probs = self.segment(image) File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 497, in segment conformed = self.preprocess(image) File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 469, in preprocess print('The input image has resolution (%4.2f,%4.2f,%4.2f) mm, but 1mm-isotropic input is required.\n' TypeError: only size-1 arrays can be converted to Python scalars How can i solve this?

2 1

(no subject)
by fsbuild 23 Sep '22

23 Sep '22

External Email - Use Caution Sorry if this is a repeat email from last night, but signal 9 can mean you ran out of memory.  You should try allocating more memory to the VM.. You could also try running the latest freesufer version = 7.3.2 which is compiled for Ubuntu 20 and you can get from, https://secure-web.cisco.com/1qqb_N_CupmU2BzFF50PfaJo-Ylza_cis45…  I would uninstall 7.1.1 if you are going to try 7.3.2, but a different version won’t make a difference if you are running short on available RAM. - R. On Sep 23, 2022, at 09:50, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:not sure what is going on. It received a kill signal (the 9 mentioned at the end). This often means that it was killed externally. Does this happen repeatedly? Does this happen on other subjects? How much memory did you allocate to your virtual box?On 9/23/2022 1:04 AM, Ahmad Khan wrote:        External Email - Use Caution         Dear Free Surfer Development Team.I am using the recon -all command to compute the volume of different regions of the brain. I am running the free surfer version freesurfer-linux-centos7_x86_64-7.1.1-20200723 on Ubuntu 20.4 installed on a virtual box. I am getting the following errors and the log file is also attached with this email. ERROR: mri_ca_register with non-zero status 137Your timely response would be highly appreciated.Best Regards Dr. Ahmad Raza Khan(Ramalingaswami Fellow)Center of Bio-Medical Research (CBMR)SGPGI Campus, Raibareli RoadLucknow-226014, UP, INDIA_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/15PFLqzDL1HVPjQsEm2xIbfuOh37ckPLkKOr9B6nfzZplq… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Running v7 with recon-all v6 files
by Alexandra Brouillard 23 Sep '22

23 Sep '22

External Email - Use Caution Hi I ran recon-all on an external server using the version 6. I recently downloaded the v6 on my Mac v12.6. I was able to set a home directory but get a ‘permission denied’ error when typing ‘$FREESURFER_HOME’ (but have the permissions/sudo). I also can’t open Freeview: by double clicking on the app, the GUI crashes, or by typing ‘freeview’ in the terminal I get a PETSC error. According to some previous forum threads, I’m thinking of downloading the v7 but would like to validate that it’s OK when using recon-all v6 files. Thank you for your support, Alexandra

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer