Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30067 discussions

06 Aug '23

External Email - Use Caution Hi expert, I found an issue when I do skull stripping. I used the following command line. recon-all \ -skullstrip \ -s fs_output \ -clean-bm \ -wsthresh 100 But, I found too much brain tissue has been removed, particularly for the visual and motor cortex (almost the entire visual cortex has been removed). Do you have any thoughts about this issue? Even though I tried wsthresh=100, it's still not working. I am not sure how I can include all of the brain tissues. Thanks. PS. I am trying to attach a screenshot to show the skull stripping results, however, I found the message with figure has been filtered. So, I have to post this question without any figures. I am not sure whether I clarify my question. Can I post any questions by showing screenshots? Best, Cain

2 3

How is cache.th40.pos.sig.voxel.mgh computed, exactly?
by Mark Ebden 04 Aug '23

04 Aug '23

External Email - Use Caution Hi, I was wondering if anyone knows how the numbers in cache.th40.pos.sig.voxel.mgh are computed, or where I'd look to learn this. There is a one-liner in the documentation<https://secure-web.cisco.com/1R2vQZUhHj-zAreoIH8kMlOuUPh5jYx8TyPmfmDzbM1Dl-…> but I'd like the mathematical details of the correction etc. so I can determine what the final numbers (from 0 to 1) represent. I've noticed from browsing the plot in FreeView that significant areas have values close to 1, which is puzzling. Thanks if you could point me in the right direction. Kind regards, Mark Mar [cid:b7c6e65e-f85e-4206-aaa0-1ec00aa2fde2] Mark Ebden, D.Phil (Pronouns: He/Him) Research Analyst The Hospital for Sick Children 555 University Ave, Toronto ON M5G 1X8 P 416.888.0841 [cid:3b077a75-32bb-46ed-b1d2-b74379e6a8d1]<https://secure-web.cisco.com/17-WtJwO2uIWyZ7umzDRCiH0I5Q1NZ-tfYcx_zx9tznEDb…> ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

2 6

freeview (visualize pial and white surface)
by DS 04 Aug '23

04 Aug '23

External Email - Use Caution Hi experts, I have a question about freeview. Recently, when I loaded lh.pial and lh.white at the same time, the freeview was suddenly aborted and reported the following error. ../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion `used_next <= save->vertex_store->buffer_in_ram_size' failed. But, if I only load lh.pial or lh.white separately, I found it’s working. I guess there might be inconsistent parameters between the two files, because when I check another subject, both files can be visualized. Do you have any thoughts about this issue? Thank you so much for any suggestions.

2 3

Re: [Freesurfer] error in my software
by fsbuild 04 Aug '23

04 Aug '23

External Email - Use Caution  Hello Mikel, Can you send us more details like terminal output or perhaps screenshot from the terminal that shows the error ? - R. On Aug 4, 2023, at 15:54, MIKEL GARCÍA AGUIRRE <Mikel.Garcia(a)alu.uclm.es> wrote:        External Email - Use Caution        Hello,I am working with a MacBook M1 from 2020 and I downloaded two versions of Freesurfer. The first one was the 7.4.1 version, but I have also tried the 7.2.0 version. The problem that I have is that whenever I tried to upload one file, the program directly produces a force quit and I can not work with it. Do you have any recommendations for fixing this problem?Looking forward to hearing from you,Best regards,Mikel_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

error in my software
by MIKEL GARCÍA AGUIRRE 04 Aug '23

04 Aug '23

External Email - Use Caution Hello, I am working with a MacBook M1 from 2020 and I downloaded two versions of Freesurfer. The first one was the 7.4.1 version, but I have also tried the 7.2.0 version. The problem that I have is that whenever I tried to upload one file, the program directly produces a force quit and I can not work with it. Do you have any recommendations for fixing this problem? Looking forward to hearing from you, Best regards, Mikel

1 0

Is there an inverse function to mris_flatten?
by Phillip Tran 04 Aug '23

04 Aug '23

External Email - Use Caution Hello FreeSurfer team, I'm new to FreeSurfer and would greatly appreciate your help. My objective is to reverse the flattening process of mris_flatten. I successfully got flatmaps by using mris_flatten on "bert" inflated hemispheres with manual relaxation cuts (in Freeview/tksurferfv as opposed to deprecated tksurfer) as directed by these instructions: https://secure-web.cisco.com/1A7xoXmR8WDKrZnRfFGHzLvRwUtKyRcCICrInChTpRemfC… I also have a small 2-D patch of non-MRI image data that's been registered to and fused with the hemisphere flatmap. Is there an inverse function or procedure for mris_flatten? E.g.: I would input a .dcm/.jpg/etc. containing the patch-fused flatmap, then get in response the original inflated hemisphere with the fused patch appropriately deformed to fit the 3d shape. Then, is there potentially a way to return the patch-fused inflated hemisphere back into the pial surface from which it was inflated? FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Ubuntu version: 22.04.2 Jammy Jellyfish Thank you for your time, Phillip

2 1

using synthsr with HCP Pipeline
by KennethSPrice 03 Aug '23

03 Aug '23

External Email - Use Caution Hello all, I am currently struggling through the HCP Pipeline! I want to use clinical scans processed with synthsr in the HCP Pipeline. 1.) Is this even possible? 2.) Is there a way to get a T2 output with synthsr? 3.) In lieu of the HCP Pipeline, could you use SythSR scans with the HCP Database to do a normal group analysis? Thanks, Ken

2 1

[FreeSurfer] recon fix the surfaces of the brain
by Krystal Xiwing Yau 03 Aug '23

03 Aug '23

External Email - Use Caution Dear FreeSurfer experts, I am fixing the error generated by recon-all. Please see the capture below: [cid:a7289c63-1b2b-407c-9dec-a9ff5e082daa] Fig.1 Under-segmentation of white and pial surfaces still not fixed after running the command with the flags -autorecon2-cp -autorecon3 for the subject [cid:baf96016-01d2-4d50-ac8e-ce6067c1dec6] Fig.2 The same image for the subject, with the visible wm. The tutorial <https://secure-web.cisco.com/1eFs9sHrAZSKhe4nUQhj-OHr9PCuaQnsYS1AVa0FxCl5k_…> from the FsTutorial indicated that adding control points to the white matter area only. Moreover, the pial surface expends from the white surface. Thus, it is not possible to add control points on the cortex. Would somebody can help with fixing such error, please? Thank you very much! Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

2 5

7 zip pass code please
by Lewis, Jeramy 02 Aug '23

02 Aug '23

External Email - Use Caution Hello, I am stuck downloading and installing freesurfer. It is requiring a pass code to open the 7zip file to install. Please provide the pass code so I can continue. Jeramy Lewis, PhD Mallinckrodt Institute of Radiology Washington University School of Medicine 4525 Scott Ave, Room 3224 G St. Louis, MO 63110 mobile: 720-885-2044 e-mail: jeramy(a)wustl.edu<https://secure-web.cisco.com/14UiD4O4jlVflixdtoLKMb1QHbpWKEUDpJyazsQNyeP99x…> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

1 0

Freeview sudden termination
by Jacob Bunyamin 02 Aug '23

02 Aug '23

External Email - Use Caution Hi, I am running freesurfer/7.3.2 and had an issue with freeview sudden termination. The error message is *sub-002/label/aparc.annot.ctabMRISreadAnnotationIntoArray: vertex index out of range: 538980362 i=2020300A, in_array_size=132205* *annot file: /fs04/wr47/Project/Data/NIFTI/Freesurfer7.3.2/sub-002/label/aparc.annot.ctab* *terminate called after throwing an instance of 'int'* It happened when I tried to load any annotation. I can load pial surfaces. I worked in a cluster computer if that helps. Thank you, Kind regards, Jacob -- *Jacob Bunyamin* PhD Student *Department of Neuroscience* Central Clinical School, Monash University 99 Commercial Road Melbourne VIC 3004 *E:* jacob.bunyamin(a)monash.edu

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Freesurfer