Freesurfer

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17 participants
30086 discussions

Comparing surface maps
by Fotiadis, Panagiotis 11 Aug '20

11 Aug '20

External Email - Use Caution Hello FS experts, I have a cohort of subjects for whom I created cortical thickness and T1w/T2w signal ratio surface maps, projected them to fsaverage’s surface, smoothed them, and then created average thickness and T1w/T2w maps using mris_preproc. Is there a way to statistically compare the two averaged surface maps (i.e., come up with a third surface map displaying correlation patterns between thickness and T1w/T2w signal across the surface)? Thanks in advance! Best, Panos

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Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Medial Nucleus Errors
by Angel Hammond 11 Aug '20

11 Aug '20

External Email - Use Caution Hello Freesurfer Experts, I wanted to re-post a portion of a question that a previous team member posted on June 20th, 2019 (See: Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors) We have visually checked 116 subjects that have been processed using Freesurfer's latest hippocampal/amygdala subfield segmentation algorithm (Development version 20180518 <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…>) and came across a few cases that had questionable segmentation. The T1s had were processed using FS 5.3, and we used the command "segmentHA_T1.sh" from the latest Dev version. -We have come across about 5 subjects' medical nuclei masks that are located in the Putamen region (more superior/detached from the rest of the amygdala) on one side of the brain (in some cases just the right side, in other cases just the left side). In all of the other subjects, we don't see that same detached looking segmentation into the putamen on one side as these few show. I will attach screenshots to show this. -I have checked the aseg for these subjects as suggested in the previous question, and the hippocampus, amygdala, and putamen all look fine there. I have also checked the output volumes for the medial nucleus of these subjects and the numbers all look fine. -So, my main question is: If the placement of the medial nucleus is wrong in the segmentation (detached/in the putamen as shown) but the aseg looks correct, can we still use those values reliably? Thank you! Angel Hammond Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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Longitudinal image processing - Error at 3rd step
by Albulena Shaqiri 11 Aug '20

11 Aug '20

External Email - Use Caution Dear all, I am very new to freesurfer so I might be asking an obvious question and I am sorry about that. I tried to find this in the archives but did not find a solution. I am have done the following steps successfully for images at t0 and t1 while doing the longitudinal processing but I am stuck at the 3rd step: *First step: * recon-all -subject 01_t0 -i /subjectfiles/t0/sanlm_13.nii -all -qcache -notal-check recon-all -subject 01_t1 -i /subjectfiles/t1/sanlm_13.nii -all -qcache -notal-check *Second step**: * recon-all -base 01_t0t1template -tp 01_t0 -tp 01_t1 -all *Third step (Where I have an error): * recon-all -long 01_t0 01_t1 01_t0t1template -all ERROR: Flag 01_t0t1template unrecognized. -long 01_t0 01_t1 01_t0t1template -all Linux heds-s008 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thanks in advance, Alba

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Brain/head size Correction Clarification
by Purcell, Juliann 11 Aug '20

11 Aug '20

External Email - Use Caution Hello FreeSurfer experts, I’m planning to run an analysis using mri_glmfit in the command line to look at relationships between cortical gray matter volume and indices of adolescent substance use. Do I need to include brain/head size as a covariate in these analyses even though they are performed in the conformed space of fsaverage and not in native space? I suspect the answer is yes, but in looking through the archive many of the questions pertained specifically to subcortical analyses or those performed in QDEC so I wanted to clarify for cortical volumetric analyses. Thank you for your help! Best, Juliann Purcell, MSc Doctoral Candidate Medical/Clinical Psychology Doctoral Program University of Alabama at Birmingham Department of Psychology juliannp(a)uab.edu<mailto:juliannp@uab.edu>

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freesurfer7.1.1 hippocampal subfields matlab crash
by Ron Killiany 11 Aug '20

11 Aug '20

External Email - Use Caution I see that others have posted on this but not necessarily the fix. I'm happy to test anything out that I can with it. I'm using MacOS running 10.15.6. I was having problems with matlab crash so I removed old versions of freesurfer from this machine and did a clean install of Freesurfer 7.1.1 and added the Matlab 2014B files. Set up freesurfer and was able to successfully run one scan through the sengmentHA_T1.sh but an identical second scan failed with a MATLAB fatal error. Any subsequent run also failed. In these attempts I only tried to run one case at a time, no other activity on that computer. Before the clean install, I was able to run about five scans through the process before the matlab fatal error appeared and no other scans would run. Crash dumps and script is enclosed if they can be of any help. I welcome any suggestions that you may have - thank you for your help with this. --ron -- Ronald J. Killiany, Ph.D. Center for Biomedical Imaging Departments of Anatomy & Neurobiology, Neurology, Radiology and Environmental Health Boston University School of Medicine and Boston University School of Public Health 700 Albany Street, W701 Boston, Massachusetts 02118 *phone: 617-358-8276* fax: 617-638-4922

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Problem with recon-all command in tutorial dataset
by Wei Shao 11 Aug '20

11 Aug '20

External Email - Use Caution Hi, Freesurfer Team My name is Wei Shao, I just a beginner of Freesurfer. As I play around with the tutorial data, here is a problem I met, I tried to recon-all the dicoms data as the tutorial instruction practice with the date instructed, but it always reports like the SUBJECTS_DIR directory does not exist. [shao@WeiS ~]$ export TUTORIAL_DATA=tutorial_data [shao@WeiS ~]$ export SUBJECTS_DIR=$TUTORIAL_DATA/practice_with_data [shao@WeiS ~]$ cd $SUBJECTS_DIR/dicoms [shao@WeiS dicoms]$ recon-all -all -i I50 -s Subj001 ERROR: SUBJECTS_DIR tutorial_data/practice_with_data does not exist. [shao@WeiS dicoms]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: tutorial_data/practice_with_data does not exist FREESURFER_HOME /usr/local/freesurfer/7.1.0-1 FSFAST_HOME /usr/local/freesurfer/7.1.0-1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR tutorial_data/practice_with_data MNI_DIR /usr/local/freesurfer/7.1.0-1/mni [shao@WeiS dicoms]$ pwd /home/shao/tutorial_data/practice_with_data/dicoms [shao@WeiS dicoms]$ What I should do to fix this problem, Thanks in advance. Best, Wei

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Question about obtaining stats from a gtm file
by Gary Tan 10 Aug '20

10 Aug '20

External Email - Use Caution Hi freesurfer mailing-list, I am trying to use asegstats2table to combine the individual gtm.stats.dat files. I assume that the output is mixed up because these gtm files have no column labels. Below is the command I used: asegstats2table --inputs subject1/gtmpvc.output/gtm.stats.dat subject2/gtmpvc.output/gtm.stats.dat --meas mean --all-segs --tablefile test_stats_pvc.txt Is there a way to tweak the asegstats2table command to get the gtm.stats.dat files from different subjects stacked into a single file? Freesurfer 6.0 is the version Platform is Ubuntu 16.04 Sincerely, Gary Tan

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Re: [Freesurfer] Freesurfer Digest, Vol 198, Issue 18
by Ana Navarro Cebrian 10 Aug '20

10 Aug '20

External Email - Use Caution Yes, WUSTL format. I saw some ifh files in the average directory of freesurfer (at least the version I downloaded) so I thought there was maybe a way to view or convert those types of files. On Mon, Aug 10, 2020 at 12:01 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: img (with ifh header) to mgz (Douglas N. Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 10 Aug 2020 11:33:54 -0400 > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] img (with ifh header) to mgz > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <472e39b7-8a08-f585-8d52-0c748e792395(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > what is ifh? Interfile? I don't know how to convert ifh > > On 8/10/2020 10:57 AM, Ana Navarro Cebrian wrote: > > > > ????????External Email - Use Caution > > > > Hi all, > > > > How can I view an .img or convert it to .mgz? I've used .img files > > with freesurfer, but their headers had a .hdr extension. In this case, > > the header has an .ifh extension and I'm not able to view the image in > > freesurfer. > > > > Thanks! > > > > -- > > *Ana Navarro-Cebrian, PhD.* > > Assistant Research Scientist > > Psychological and Brain Sciences Department > > Johns Hopkins University > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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img (with ifh header) to mgz
by Ana Navarro Cebrian 10 Aug '20

10 Aug '20

External Email - Use Caution Hi all, How can I view an .img or convert it to .mgz? I've used .img files with freesurfer, but their headers had a .hdr extension. In this case, the header has an .ifh extension and I'm not able to view the image in freesurfer. Thanks! -- *Ana Navarro-Cebrian, PhD.* Assistant Research Scientist Psychological and Brain Sciences Department Johns Hopkins University

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high pass filter cutoff
by Nasiriavanaki, Zahra 10 Aug '20

10 Aug '20

Hi Freesurferers Could you please let me know how I should calculate the high pass filter cutoff? I have seen a bunch of different formulas (i.e 1.5*the stimulation period)? My task is a block-designed task, each stimuli takes 16 seconds and is followed by the next stimuli without an ITI. TR=2, number of conditions=8. I have used a hpf=0.01, Is this correct? Thanks Mona

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