Freesurfer October 2021

freesurfer@nmr.mgh.harvard.edu

81 participants
113 discussions

Creating a surface parcellation from a volume atlas
by Paul Dhami 18 Oct '21

18 Oct '21

External Email - Use Caution Dear Freesurfer community, I have a .nii volume atlas (CAREN), defining 5 networks, in MNI (ICBM152) space. However, I wish to do my analysis in surface rather than volume space, and for the software I am using, that means I need to load in a .annot file. For the first step, I used: mri_vol2label --c CAREN_5networks.nii --id 1 --l 1.label and did this for values 1 to 5 (for each of the networks). However, looking at the resulting label file, the first column is nothing but -1 values. I believe this should be the vertex number, and trying to combine these labels into an .annot file is not working. Apologizes for the naive question, but can anyone share as to how I can ultimately create a surface atlas when I have the volume.nii atlas file? Was I wrong with mri_vol2label as my first step? I am using Freesurfer version 7.2.0. Thank you, Paul

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Question about 'thickness.fwhm10.fsaverage'
by Dongyue Zhou 18 Oct '21

18 Oct '21

External Email - Use Caution Dear FreeSurfer experts: I use the 'qcache' command to get the file '$SUBJECTS_DIR/subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh'. Now,I have known that cortical thickness in this file is in standard space.But I don't understand why it is an average of 40 subjects. Is it not CT measures an individual in standard space? I can get cortical thickness in each vertice by reading this file in matlab. And I know mean CT is computed by dividing sum CT of all ROI vertices by the number of ROI vertices. Is there any way I can get individual ROI in standard space if I want to compute mean CT measures of each ROI? or Can I use file '$SUBJECTS_DIR/fsaverage/label/?.annot' as atlas directly?

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Problem with intensity normalization control points
by Staci A Board 18 Oct '21

18 Oct '21

External Email - Use Caution Hello, our lab has been using freesurfer for years, dating back to version 4.3 and recently ran into a problem with a new installation of 7.2. After adding control points in the typical fashion and saving them into the subject’s tmp folder as “control.dat” and running -autorecon2-cp, mri_normalize seems to correctly identify the control points, the correct number, the mean value and the scaling. The subsequent steps complete without failure and brain.mgz is generated with 110 values in the cp spots. However, the subsequent wm.mgz and brainmask.mgz images do not seem to have been affected by the control points (e.g. the control point locations aren’t at a 110 value and the white matter is almost identical). Curious if anyone else has run into the issue? Is there a new workflow in this version of Freesurfer that I’m neglecting? So far I have tried to create a new control.dat using freeview and copied the old points into that file, and run twice with the same results.

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Postdoctoral Fellowship
by Didenur Sahin 18 Oct '21

18 Oct '21

External Email - Use Caution Dear All, Brain Development And Psychosis Lab, is pleased to announce the opening of a postdoctoral fellowship position in clinical neuroscience and cognitive neuroimaging. Please take a look at the attached advertisement. Best, Didenur Sahin *ANNOUNCEMENT OF POSTDOCTORAL FELLOWSHIP IN FMRI ANALYSIS * Brain Development And Psychosis Lab, National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Centre (ASBAM) & Department of Psychology, Bilkent University, Turkey. The Brain Development And Psychosis Lab is pleased to announce a postdoctoral fellowship position in fMRI analysis. Located within the National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Centre (ASBAM), the Brain Development And Psychosis Lab conducts research in adolescent brain development. The lab's primary mission is to understand the cognitive, neurobiological, and genetic mechanisms that influence an individual's susceptibility to develop serious mental illness (e.g. psychosis, schizophrenia). We seek a candidate with experience in f-MRI analysis. A Ph.D. in cognitive science, engineering, neuroscience, or related field is required. Experience in computational methods used in neuroimaging (e.g., Matlab, Python, SPM) and computer programing is also required. Advanced skill in statistical modeling, and the ability to carry out independent statistical analyses using standard software packages (e.g., SPSS, SAS, R) are desirable. The candidate will have the opportunity to analyze and interpret f-MRI data from an ongoing project on brain development, which aims to provide neurobiological insights into the genetic and environmental mechanisms of risk around the time of life when psychotic symptoms typically appear. The project is funded by The Scientific And Technological Research Council Of Turkey (TUBITAK). Postdoctoral fellows will receive mentoring in clinical/human research methodology and work in a collaborative, multi-disciplinary environment to gain experience in psychosis-centered research. The postdoctoral fellowship position is for 18 months, renewable subject to securing further funding. Please email a CV and cover letter to Prof. Dr. Timothea Toulopoulou (ttoulopoulou(a)bilkent.edu.tr) -- Didenur Şahin Ph.D. Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) Bilkent University Ankara, Turkey 06800

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FW:
by CHM Recruiting 17 Oct '21

17 Oct '21

External Email - Use Caution Hello, Can you please post the attached to the Freesurver (listserv)? Research Specialist, UW- Madison, WI, Center for Healthy Minds.<https://secure-web.cisco.com/1A_r9pG3lSDyZYMJsUtVNwH5A1tgFpm8iz07A00PeWU88F…> Thank you, Lisa A. Wesley Pronouns:<https://secure-web.cisco.com/1VbRVY9T5mcFGkLyNTqXDa7YSwOekf5hem7tT8KZzaUKj_…> She/Her/Hers Human Resources Generalist 608/262-0196 lawesley(a)wisc.edu<mailto:lawesley@wisc.edu> [cid:image001.jpg@01D7C36A.8DD846B0] P Please help conserve by considering if it is necessary to print this e-mail

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Hypothalamic segmentation
by AJ 17 Oct '21

17 Oct '21

External Email - Use Caution Hi, How does one normalize the data output from hypo_seg for the head size, with sbTIV or eTIV, which are a bit different from each other. Many thanks AJ

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Synthsr
by Castro Leal, Gonzalo 14 Oct '21

14 Oct '21

External Email - Use Caution Hello FreeSurfer, I am trying to run the following comand: :~$ synthsr --i $SUBJECTS_DIR/super_resolve/ --o $SUBJECTS_DIR/super_resolved/ --ct --threads 4 --cpu synthsr: command not found Is this due to the synthsr being broken or with my installation of freesrufer developers edition? Many thanks, Gonzalo.

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Re: [Freesurfer] A question regarding a Freeview command (Douglas N. Greve) 8/10/21
by inbal paran 14 Oct '21

14 Oct '21

External Email - Use Caution Dear FreeSurfer developers, First, thank you Douglas very much for your reply. I have a follow up question, and for some reason I wasn't able to continue the thread, so I have copied the thread with Douglas's answer and my first question below. Here is my followup question: I did the ROI analysis, asegstats2table and mri_glmfit with --table option as you suggested, but the thing is that I want to visualize my significant results using Freeview, how can I do that? Also - by any chance can you tell me how can I continue the thread? When I am entered the archive I tried to click on "reply via email to.." but that just opens the outlook as a default and I don't work with outlook. For some reason I can't open the thread using gmail. Thank you very much, Best, Inbal Message: 7 Date: Fri, 8 Oct 2021 12:51:42 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] A question regarding a Freeview command To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <bd3f5853-edf3-270d-9d1e-8c6f65d55420(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" The volume is the volume of cortex only, not the volume of subcortical structures. We don't have a VBM-style analysis that would be needed for subcortical GM. You can always do an ROI analysis, asegstats2table and mri_glmfit with --table option; this will allow you to analyze the volume of each structure as a single number, not a map. To answer your question, your freeview command line does not need to change. On 10/4/2021 2:27 AM, inbal paran wrote: > > ????????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 (*MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1vcxvE4KyDsi4qqXPfbLdF0-Ec-nWSe90uzyY86VVnWLhO… > < 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/1_uWMvw0JQHDbRb3qSmM-v2YM-E0oQrb6OCiSvXSQcDnOGy…> > < 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. > Thanks again for your help, Inbal -- *Inbal Paran, M.PT <http://secure-web.cisco.com/1GATqktVB9GCv-D6rmlzLZKLrLOjzGIDyvhTd6-WnB7r0cQ…>.* 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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Segmentation of thalamic nuclei - misplaced position
by Edyta Leks 14 Oct '21

14 Oct '21

External Email - Use Caution Hi Freesurfer expert, I have a question regarding the segmentation of thalamic nuclei. I processed 15 subjects with freesurfer v6 (recon-all) and additionally, ran the thalamic segmentation implemented in FreeSurfer. Then, I wanted to use the label of the thalamic nuclei to select an ROI in the VM, VPL and in other nuclei to perform the ROI analysis in SPM. Therefore, I converted the outputs of the segmentation (ThalamicNuclei.v12.T1.mgz) into nifti files by using the command "mri_convert .mgz .nii". Additionally, using ImgCal in the SPM, I created a mask for each nuclei separately. Most nuclei look great and correspond to their anatomical position. Unfortunately, the position of some nuclei is completely wrong. For example, the size of the VM (left) is definitely too small and the position seems to be on the border / outside of thalamus (attached files and link). I do not see the right-VM at all. This issue affects all my data as well as data analyzed in another institute. In the attached picture (Thalamic_segmentation_VMleft.png), blue represents the VM. We can clearly see that the position as well as the size is completely incorrect compared to the known anatomical position or shown in your publication. Could I ask for an explanation and help in solving the problem. The parameter for T1 and T2 scans: T1: 208slices, voxel size=0.8mm isotropic, TE=3.16ms, TR=2400ms, BW=220Hz/px, ES=7.5ms T2: 208 slices, voxel size=0.8mm isotropic, TE=5.63ms, TR=3200ms, BW=744Hz/px, ES=3.52ms Here you can find all the files: https://secure-web.cisco.com/1KtaGTX0Nfx2jwZl-X1QkJstv6OQtmYKCMAYA5rzu-lXHK… Best regards, Edyta Leks Edyta Leks High Field MR Center Max Planck Institute for Biological Cybernetics Max-Planck-Ring 11 72076 Tübingen Germany ________________________________________________ office: 4.B.06 tel: +49 7071 601 918 e:mail: edyta.leks(a)tuebingen.mpg.de

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Re: [Freesurfer] Comparing volumes before and after editing, and aparc+aseg after rerunning recon-all
by Kang, Jee Won 13 Oct '21

13 Oct '21

External Email - Use Caution Thank you for your reply! It was very helpful. I was able to successfully create the difference mask according to your instruction. As far as the sum.dat output from mri_segstats, I'm uncertain as to what columns to look at to find the percent of each ROI that had edits; all I get is information regarding the number of voxels, and the mean, stdDev, min, max, and range of intensity for each structure. To provide some more context, the goal of this endeavor is to essentially create a sort of "log" of edits, to know the regions where voxels were erased or added (and to which volume). In terms of identifying only edited regions, would it be better to create a mask which extracts only voxels with a value of 1 or 255? Also, I had a question regarding a different topic with regards to to aparc+aseg.mgz after rerunning recon-all: although the pial surface changed after rerunning recon-all, the aparc+aseg.mgz didn't seem to change. I've attached a screenshot where you can see the aparc+aseg extending significantly beyond the pial surface, so I'm wondering why that might be, and whether it's a problem? In the troubleshooting slides it does mention that it's okay if the cortical ribbon extends beyond the surface, since the ribbon isn't used for anything, but why would it not change to reflect changes in the pial surface? Thank you very much again for your assistance. -Jee Won ________________________________________ Date: Fri, 8 Oct 2021 12:48:03 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Comparing volumes before and after editing To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <8558ace1-9ef4-a75c-984b-1b53cc87e2ea(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" If you subtract them, eg, fscalc vol1.mgz sub vol2.mgz abs gte 0.5 -o diff.mgz This command will subtract the two, take the absolute values, then threshold (binarize) the differences. I'm not sure what you are looking for in terms of aparc+aseg, but you can do something like mri_segstats --ctab-default --seg aparc+aseg.mgz --excludeid 0 --i diff.mgz --sum sum.dat and sum.dat will tell you the percent of each ROI that had edits On 10/1/2021 4:01 PM, Kang, Jee Won wrote: > > ????????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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1tDN495Zmz69_tS_DgP3uRxsUNUoW4dfYipN6gNbM54T8s…

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Freesurfer October 2021