Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

overlap/intersection of labels?
by Dr. Cornelius Kronlage 22 Feb '21

22 Feb '21

External Email - Use Caution Dear freesurfers, is there an elegant way of computing the intersection or overlap of different labels or - which would be even more useful for my application - annotations? I only managed to find labels_intersect (which appears to be from https://secure-web.cisco.com/12D3ntbm8RDBV366hh41UjEkFWk2mrjQHSMiY8WEom0naU… ) which is awfully slow. In case this is of use for anyone else, I attached a modified version using 'join' that runs much faster, only has some compatibility issues with Mac. >time labels_intersect precentral.label frontal.label out1.label > /dev/null real 1m41.862s user 0m31.052s sys 0m30.757s >time bash bash_labels_intersect.sh precentral.label frontal.label out2.label real 0m0.193s user 0m0.118s sys 0m0.015s >diff -w out1.label out2.label > Thank you and best wishes Cornelius -- Cornelius Kronlage Assistenzarzt Klinik für Neurologie | Neurologie mit Schwerpunkt Epileptologie Universitätsklinikum Tübingen Hoppe-Seyler-Str. 3 | 72076 Tübingen

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Hippocampal subfield segmentation by T2 scan
by Wei Shao 19 Feb '21

19 Feb '21

External Email - Use Caution Hi, dear Freesurfer team I used sagittal T1(MPRAGE-sag_T1w.nii.gz) to recon-all and did the hippo-subfield segmentation on T1, but when I tried to use the additional scan by segmentHA_T2.sh : segmentHA_T2.sh sub-AVP14352 /home/weishao/sub-AVP14352/Ses-01/anat/sub-AVP14352_ses-01_cor_run-01_T2w.nii.gz sub-AVP14352_T2 0 Here is the feedback Error using kvlGEMSMatlab std::bad_alloc Error in kvlReadCroppedImage (line 11) Error in segmentSubjectT2_autoEstimateAlveusML (line 930) @#@FSTIME 2021:02:19:13:38:45 run_segmentSubjectT2_autoEstimateAlveusML.sh N 18 e 385.18 S 24.62 U 646.85 P 174% M 1033292 F 130 R 2612883 W 0 c 193519 w 290275 I 2443704 O 429952 L 3.35 3.58 5.40 @#@FSLOADPOST 2021:02:19:13:45:10 run_segmentSubjectT2_autoEstimateAlveusML.sh N 18 5.71 5.26 5.58 Linux gra-login1 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 GNU/Linux T2 hippocampal subfields exited with ERRORS at Fri Feb 19 13:45:11 EST 2021 Could you tell me what I should do to fix this? Thanks Best, Wei

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multiple comparisons correction
by Agurne Sampedro Calvete 19 Feb '21

19 Feb '21

External Email - Use Caution Dear Freesurfer experts, I am doing a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment). I have followed the group analysis tutorial ( https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mY… ), where it is suggested to do a Z Monte Carlo simulation with the following command: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces However, I have two questions regarding this issue: 1) I would like to know whether is it correct to use for example --cache 3 or 2 instead of 4. Is it recommended? 2) Is it better to use, instead of the above Z Monte Carlo simulation command, a permutation with the following command?: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1 Is it appropriate to use any of both? I do not know which is more recommended or whether both are adequate so I can simply choose, for example, the first one. Thank you very much in advance. Kind regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015)

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3 groups comparison question (mri_glmfit)
by 김용갑 19 Feb '21

19 Feb '21

External Email - Use Caution Deer Freesurfer Experts, We are trying to perform 3 group comaprison analysis in Freesurfer (mri_glmfit). Our fixed factors are "group (Case1, Case2, Healthy)" and our dependent variables are "thickness variables".We want to control "CPZ" continuous variable but CPZs of healthy group are all zero.So, it makes following errors in Freesurfer 1. ill-conditioned problem, Freesurfer design matrix maybe be linearly-dependent 2. Badly scaled problem, CPZ variables are higly different between groups (Case1, Case2 have big CPZ variables, but Healthy have all zero) To solve this problem, we are going to make own design matrix using only two indicator varibles for three groups.(Freesurfer's design matrix seems to use three indicators, which may make error in this analysis)And we are going to change the contrast to suit my design matrix with two indicators. Is it possible to use two indicator design matrix in Freesurfer to perform 3 group comparison analysis(mri_glmfit)?mri_glmfit help page said that the design matrix can be specified in matlab4 format, can't in excel?, Shoud it be version 4 in the matlab?Finally, to solve badly scaled problem, can i use z-score calculated on all group samples? Best regards, Yonggab Kim

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convert BA probability labels to volume
by julienbesle 19 Feb '21

19 Feb '21

External Email - Use Caution Hello, I'm trying to convert label files containing probability values for Brodmann areas (e.g. rh.BA1_exvivo.label) to volume files using mri_label2vol. I'd like to keep the probability value that's in the 5th column of the label file into the volume, but mri_label2vol sets all voxels in the label to 1 (i.e. creates a mask). Is there a way to do this? Thanks Julien -- ------------------------------------------------------ Julien Besle Assistant Professor Department of Psychology Faculty of Arts and Sciences American University of Beirut Riad El-Solh / Beirut 1107 2020 Lebanon Jesup Hall, Room 103E Tel: +961 1 350 000 ext. 4927 -----------------------------------------------------

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Queries in qdec
by Koustav Chatterjee 19 Feb '21

19 Feb '21

External Email - Use Caution Dear Forum members, May I get your help please to resolve 2 queries below? 1. I am unable to see .tiff files taken through 'quicksnaps.tiff' of the 'qdec' analysed data. Even after completing the process of 'quicksnaps.tiff' successfully, I can see only black screen while opening the file. Please find a sample pic of how those files look. [image: image.png] 2. I am using FreeSurfer version 6 where I am *missing 'Design Matrix Type'* inside the 'design' tab of 'qdec' command. [image: image.png] Thank you for your time and help. Regards, Koustav

2 1

Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS
by Ishi Tandon 18 Feb '21

18 Feb '21

External Email - Use Caution Hello experts, I have recently installed freesurfer on Ubuntu 20 (which is on virtualbox). I want to use hippocampal subfield segmentation in freesurfer. I have installed MATLAB run time (2014b) through the following command - fs_install_mcr M2014b However, this displayed the following warning - on the target computer , append the following to your LD_LIBRARY_PATH environment variable : /tmp/tmp.HvgiEwe6Av/install-target/v84/runtime/glnx864://tmp/tmp.HvgiEwe6Av/install-target/v84/bin/glnx864://tmp/tmp.HvgiEwe6Av/install-target/v84/sys/os/glnx864 Next, set the XAPPLRESDIR environment variable to /tmp/tmp.HvgiEwe6Av/install-target/v84/X11/app-defaults Having set that to the bashrc script. It gives me an error when I try the following command. segmentHA_T1.sh <https://secure-web.cisco.com/11MSQv2e7FuBi1XZjDt6ZitEBRceHDC8rRcDsdx1Fq1aC1…> bert. (error attached below). I am also attaching the changes that I made in bashrc. It would be great if you help me out. Thank you in advance. *Regards,* *Ishi Tandon* *B.tech <https://secure-web.cisco.com/1CFi-inHeHrntmx2nGqrNhbOMeLCIYQPJUzxpcsRSry9KD…> + M.tech <https://secure-web.cisco.com/1dcU_xiUsYUlrguN9SAjy7_K6ZMhQa0p9ALjneRAYlfaMX…> - Cognitive & Neuroscience* *Amity University, Rajasthan* *contact - +918239259846 ; Email- ishi.tandon99(a)gmail.com <ishi.tandon99(a)gmail.com>*

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What exactly are the BA_exvivo.thresh label and annotation files?
by julienbesle 18 Feb '21

18 Feb '21

External Email - Use Caution Hello, The ex-vivo BA label and annotation files named ?h.BA??_exvivo.thresh.label and BA_exvivo.thresh.annot seem to be thresholded versions of the corresponding probabilistic BA labels. Was a simple threshold on the probability used and if yes, what was the value? In addition the annotation files, whether thresholded or not, only have one label per vertex. Are the labels based on the maximum probability across all BA labels? Thanks Julien -- ------------------------------------------------------ Julien Besle Assistant Professor Department of Psychology Faculty of Arts and Sciences American University of Beirut Riad El-Solh / Beirut 1107 2020 Lebanon Jesup Hall, Room 103E Tel: +961 1 350 000 ext. 4927 -----------------------------------------------------

2 1

Unable to run recon all successfully !
by Sahil Bajaj 18 Feb '21

18 Feb '21

External Email - Use Caution Hello FreeSurfer experts, I am trying to run recon all pipeline on infants' brains. Somehow, out of 7 subjects, I am getting error for four subjects (S28, S69, S149 and S233) and for the other three (S36, S90 and S119) I do not see any progress in the terminal (for about the last 5 hours). Here I am attaching recon all logs for all these subjects. I would really appreciate any help. Thanks, Sahil

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Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
by Gronow, Franziska 17 Feb '21

17 Feb '21

External Email - Use Caution Dear Freesurfer experts, I've been using Freesurfer 7 for only a few months. I've searched the list and no similar observations have been reported. For my project I used the "Segmentation of thalamic nuclei" tool by Iglesias, J.E. et al. The "recon-all" as well as the thalamic segmentation process have been run. For quality control an outlier script was used to identify statistical outliers. In the course of the visual QC the PuM nucleus appeared to be mis-segmented in many cases - regardless of whether it was flagged as statistical outlier or not. I was wondering whether others had similar experiences and whether there are any recommendations how to handle such cases. We thought about excluding this area from our analysis for all subjects. Would you recommend such a procedure? I uploaded on dropbox 3 screenshots of a typical case (with/without/low opacity mask) so that you get an idea of what I mean: https://secure-web.cisco.com/13NyoIuwpnsiHWemQxkjh3X8nFYXTG9wpVXrDAWJsCjxur… Thanks for your help! Best, Franziska

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