Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30060 discussions

combining masks
by John Anderson 10 Jan '18

10 Jan '18

Dear Freesurfer experts, I want to create mask for the midbrain and the precentral gyrus. I used FSV6 to do the reconstruction. Then I used the flag -brainstem-structures in recon-all to segment the brain stem. How can I create one mask that include structures from wmpac.mgz and brainstemSsLabels.v10.mgz for instance I want to use mri_binarize to create one mask contains the following labels 1024 2024 3024 4024 from wmpar.mgz and 173 from brainstemSsLabels.v10.mgz Any advice you provide is highly appreciated. Thanks John

2 4

surfstat maps using freesurfer outputs on skull-stripped data
by Duran, Tugce 10 Jan '18

10 Jan '18

Hi FS experts, I’m running SurfStat on my freesurfer skullstriped data (recon-all with –noskullstrip flag) and getting pecan shaped brain images as shown in the attached file. Do you know what freesurfer process (make_average_subject or glm or other) is causing this issue? Thanks! Tugce Duran, B.S. Research Technologist II [cid:image001.png@01D3861A.789F16C0]<https://medicine.iu.edu/departments/neurology/research/> Indiana Alzheimer Disease Center (iADC) Office: 317-278-7015 durant(a)iupui.edu<mailto:durant@iupui.edu>

2 4

Using MRS voxel mask in freesurfer surface space
by Poortata Shirish Lalwani 10 Jan '18

10 Jan '18

Hi, We are obtaining MRS data and functional MRI data on two separate days for each subject. We use structural scan obtained during both these sessions for the freesurfer segmentation. MRS scan gives us a binary mask (nii format) in the same space as the structural image obtained during that particular scan. We want to use this binary mask during the surface based functional MRI analysis. I am not sure how to transform this binary mask to the surface space. Is there a way to do this? Best, Pia

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Is it poosible to redistribute a part of buckner_data for group work?
by Kiyotaka Nemoto 10 Jan '18

10 Jan '18

Dear FreeSurfer experts, We are planning to have a one-day neuroimaging workshop in Japan. One topic of the workshop is "FreeSurfer troubleshooting", in which we go through the online tutorial you provide ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) in Japanese language. So we would like to use the buckner_data for the workshop. However, the problem is that some have difficulties downloading the data (It takes more than 2 days to download...) So I'm wondering if we can share the part of buckner_data with attendees for the workshop in a closed network (via a site with login requirements). I read through the FreeSurfer license, and README in the buckner_data, but it doesn't mention about redistributing the data. We would like to respect the license, so could you let me know if we can redistribute the part of buckner_data? Best regards, Kiyotaka -- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Neuropsychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: kiyotaka(a)nemotos.net

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hippocampal subfields in younger populations
by Christian Krog Tamnes 10 Jan '18

10 Jan '18

Dear FreeSurfer and hippocampal subfield segmentation developers, I have noted that the FS6.0 hippocampal subfield segmentation procedure was developed using scans of older adult brains. Has the application of this method to kids, adolescents and/or young adults in any way been validated? Or do you have any thoughts regarding such use of the method? I would think this would be an issue for young kids that have markedly different brain volumes, but not for older kids and young adults that differ less dramatically from older adults. But I would greatly appreciate any input regarding this. Best regards, Christian

1 0

How to output particular area from stats subdir
by Jing Gu 09 Jan '18

09 Jan '18

Dear FreeSurfer Developers, By using the following code, we can get volume data of different areas from stats file. asegstats2table --subjects N01 --meas volume --tablefile aseg_stats.txt How can I get information of one or two areas, such as hippocampal? thanks Best, Gina

2 1

Acquiring Exact p Values
by Hannah Claussenius-Kalman 09 Jan '18

09 Jan '18

Hello, I am conducting surface group analyses and would like to acquire exact p values. The FreeSurfer manual notes that the number listed after the peak coordinates and the vertex # is a "significance value," and that the "significance in this display is a -log(10)p value, and not a straight p value." However, if I log this number the "p value" I calculate is not significant (e.g., log(5.68) = .75) so I don't believe I am interpreting their description correctly. Could you please advise on how to acquire exact p values? Thank you for your time.

2 1

Surfaces along midline
by Romella Durrani 09 Jan '18

09 Jan '18

Hi, I'm having problems with the surfaces along the midline for one scan. I have attached pictures of the brainmask with surfaces, wm.mgz, and T1 (before any of my edits). I have tried to fix this by adding control points and also tried to fix it by editing the wm.mgz file to fix the ventricle problem, however, none of these edits have resolved the issue. Thanks!

3 3

Segmentation of hippocampal subfields and nuclei of the amygdala
by Carme Uribe Codesal 09 Jan '18

09 Jan '18

Dear FreeSurfer users, I wanted to run the new script that segments the hippocampus and amygdala (segmentHA_T1.sh: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) but I can't find it in FreeSurfer 6.0. Is it already available? Where can I find it? Thanks in advance! Carme Uribe

2 2

Fail to retrievive data file from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git
by zuxfoucault Wong 09 Jan '18

09 Jan '18

Hi FreeSurfers, I am trying to build freesurfer from source on ubuntu 16.04 in order to run `recon-all -use-gpu` that is compatible with the latest cuda 9.1. I followed the instruction here to build freesurfer http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page. However, in order to `make install` I have to retrieve the data file but failed. Error message: $ git fetch datasrc error: The requested URL returned error: 403 Forbidden (curl_result = 22, http_code = 403, sha1 = 3a63ee606e817bc4c837fbc8330a16e40432f379) error: Unable to get pack index https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git/objec… error: Unable to find 3a63ee606e817bc4c837fbc8330a16e40432f379 under https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git Cannot obtain needed tree 3a63ee606e817bc4c837fbc8330a16e40432f379 while processing commit d300174e056c2e3b0188eba3fadc1d706698edac. error: fetch failed. Any suggestions? Thanks for your time! Best, Foucault

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