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30084 discussions

mris_convert orientation problem when converting from FS to .vtk
by Schumann, Aicko 04 Oct '20

04 Oct '20

External Email - Use Caution Dear Freesurfer Developers, I must admit that I have not used Freesurfer for quite some time, i.e. I may be a little rusty. I vaguely remember having the same issue a few years ago, but I cannot find anything in the forum that seems to work for me. Hence, I apologize for a potentially trivial question: I am having problems with mris_convert when trying to convert a surface from FS format to .vtk. It seems that during the conversion the orientation of the surface is somehow changed to what looks like a rotation by 90 degrees (indeed the file information seems to suggest a [x,y,z] <-> [x,z,-y] transformation). For instance, after running "recon-all" on a standard MNI152 brain (here borrowed from FSL), I want to convert the pial surfaces to .vtk format for further processing. I use the following simple command: mris_convert lh.pial.T1 lh.pial.T1.vtk Opening both surfaces in, for instance, freeview shows lh.pial.T1.vtk somewhat rotated by 90 degrees. Other target surface formats have the same issue. My suspicion is that there is some intrinsic orientation change during the conversion. How can I preserve the orientation during mris_convert? Wouldn't that be the expected behavior? Alternatively, how can I change the orientation of a surface file after the conversion? Thank you for your advice! Best, Aicko ---- Dr. rer. nat. Aicko Yves Schumann Research Assistant Professor Physicist, Center Statistician, Big Data Scientist Institute of Psychiatry Medical University of South Carolina 67 President Street (Rm. BA506C) Charleston, South Carolina, 29425 United States Phone Office: +1 843-792-6470 Phone Cell: +1 843-532-8506

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How to draw streamlines and their corresponding ROIs using freeview
by Zhiyuan Yu 04 Oct '20

04 Oct '20

External Email - Use Caution Hi, I have extracted fibers and the corresponding ROIs. I would like to know how can I draw them together using freeview. Thank you, Zhiyuan

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Queries on Freeview and opening files of 'stat' and 'surf' folders
by Koustav Chatterjee 03 Oct '20

03 Oct '20

External Email - Use Caution Dear Sir, I have stuck with two basic steps while installing FreesUrfer in my new system. May I request you to help me resolving the problem. 1. After successful completion of 'recon-all' command , a folder named as 'samplept1' has been formed under /usr/local/freesurfer/subjects. Subjectpt1 consists of different folders including 'label', 'mri', 'stat', 'surf' etc. Now, I was trying to acquire data from 'surf' and 'stat' folders. However, I am unable to open them. It seems to me a specific application is required. Please advise. 2. Could you please explain what is the purpose of having 'freeview'. Is it only only to check manually whether all the preprocessing steps such as skull stripping has been done correctly by recon-all or not? 3. I am unable to surf images one by one using "P age up and down keys in keyboard". How should I surf the images one by one? Your help is appreciated. Thank you very much. KC

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Seed ROI FC
by Lorenzo Pini 02 Oct '20

02 Oct '20

External Email - Use Caution Dear expert I'm trying to perform FC seed ROI analysis through FSfast pipeline After preprocessing I run: selxavg3-sess -s subject1 -a fsrest.surf.lh -no-con-ok -svres but I got the following error: ERROR: /bin/bash: /scratch/tp9f57a7bb_2ea1_450b_b0e8_8cdd47a2eb8b.load_nifti.m.nii: No such file or directory ERROR: loading /home/user/Desktop/test/subjects/subject1/fsrest/001/fmcpr.sm5.self.lh.nii.gz as analyze ERROR: attempting to read /home/user/Desktop/test/subjects/subject1/fsrest/001/fmcpr.sm5.self.lh ------------------------------------------ ERROR: fast_selxavg3() failed\n Moreover, I'm a bit confused how to compute whole brain seed-ROI surface map, using a pre-specified seed ROI created in orig.mgz space (sphere 5mm) Thanks in advance, Lorenzo

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QDEC command not found
by Enrico Collantoni 02 Oct '20

02 Oct '20

External Email - Use Caution Dear freesurfer experts, I installed the 7.1.1 version of freesurfer in iOS enviroment (10.15.4). I could run the recon-all without any problems. However, trying to open qdec I obtain "command not found". I've never had this problem with previous versions. Could you help me? Many thanks Enrico Collantoni

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Use ICV measures from freesurfer v7.1.0 to correct cortical volumes extracted from freesurfer v6.0
by Jayachandra Raghava 02 Oct '20

02 Oct '20

External Email - Use Caution Hello Freesurfer Developers, I have extracted ICV measures using samseg from freesurfer v7.1.0. I would like to use this measure to correct the cortical volumes that i have extracted from the same subjects using freesurfer v6.0. 1) Is it advisable to use ICV measures from another freesurfer version to correct the cortical volumes that i have extracted from the same subjects using freesurfer v6.0? OR 2) Do you advice that i should re-calculate the cortical volumes using freesurfer 7.1.0 in order to correct them using the ICV measures extracted from samseg? Nice weekend! Jay

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grey matter thickness map and SNR
by miracle ozzoude 02 Oct '20

02 Oct '20

External Email - Use Caution Hello Experts, I have a question regarding grey matter thickness map and signal to noise ratio. Does smoothing of the map increase signal to noise during surface based cortical thickness analyses? if yes or no, why? This question was asked by a reviewer in one of our manuscript because he/she thinks that one of the reasons to perform smoothing is to comply with random field theory hypotheses, when controlling for multiple testing. We did apply multiple comparison corrections using monte carlo simulation with cluster threshold of 2, 5000 iterations, and bonferroni. Thanks alot. best, Paul

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Tracula error
by Hasimoglu, Yasemin 01 Oct '20

01 Oct '20

Hi, I am trying to run trac-all using a configuration file for 30 subjects with longitudinal data, and keep getting the following errors: Too many ('s. ERROR: must specify as many DWI dicoms as subjects I looked through my file line by line and looked at similar posts on the archives but could not find a solution. I'm attaching the configuration file here. There's no trac-all.log file since this is happening at the very beginning. Any help would be greatly appreciated! Best, Yasemin Yasemin Hasimoglu Research Technician Department of Neurology Massachusetts General Hospital 149 13th St, Suite 10130B Charlestown, MA 02129

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Understanding Talairach failure detection
by Devavrat Vartak 30 Sep '20

30 Sep '20

External Email - Use Caution Hello freesurfer experts, My recon-all finished without errors, but I noticed a 'Talairach registration error' in the recon_all log. Freesurfer Ver: 7.1.1 MacOS: Mojave I followed the instructions on page '' https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview". 1) I used: freeview -v /Users/.../sub-09/freesurfer/recon_all/mri/T1.mgz -v /Users/.../sub-09/freesurfer/recon_all/mri/brainmask.mgz:reg=/Users/.../sub-09/freesurfer/recon_all/mri/transforms/talairach.xfm I am trying to understand what Talairach registration does...(See image) > should the T1 and the brainmask (lowered opacity) completely overlap one another and not be displaced? [image: Screen Shot 2020-09-29 at 22.29.01.png] 2) When I try: tkregisterfv --s sub-09/freesurfer/recon_all --fstal --surf orig > This generates the error: ERROR: cannot find /Users/.../sub-09/freesurfer/recon_all/surf/orig Is the tkregisterfv command correct? Any suggestions on how I can explore if the registration went ok and if not how to initialize tkregisterfv? Thank you. - Dev

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Right-side bias in thalamic segmentation pipeline?
by Gallagher, Evan (NGG) 30 Sep '20

30 Sep '20

External Email - Use Caution Hi all, I've been working on a project that involves the thalamic segmentation pipeline published by Iglesias et al. in 2018 in NeuroImage ("segmentThalamicNueclei.sh"). While the pipeline itself works great, we have noticed that the right hemisphere VOIs tend to have slightly larger volumes than the left hemisphere VOIs. This has been true in two separate datasets (n=24 and n=25), neither of which has an obvious physiological trait that would lead us to expect these sorts of hemisphere differences. This is my first time posting a question on this list, so I'm not sure if images are OK. If yes, there are a couple posted at the bottom of this message that should visualize what I'm talking about. If not, I can say that the volume differences are most pronounced in the largest VOIs (PuM, VPL, VLp, etc); in these regions, the right side is ~200-300 cmm larger than the left side. Additionally, the average volumes on both sides are reasonable based on Figure 8 of Iglesias et al (in the sense that our average volumes are well within the violin plots in that figure). I'm wondering if anyone has encountered this trend before, and/or if there's a correction I might implement to equalize the volumes. We want to be understand-to the extent possible-the extent to which these differences are driven by biology vs image processing. Thanks so much, Evan Images follow: [cid:image001.png@01D69732.FB8CB570] [cid:image002.png@01D69732.FB8CB570] [cid:image004.png@01D69732.FB8CB570]

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