Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Extraction of CC Labels and Conversion to FSL MNI Space
by Hua, Jessica 17 Mar '22

17 Mar '22

External Email - Use Caution Hi FreeSurfer, I am trying to extract CC subregion labels from aparc+aseg.mgz (ids: 251-255) into a format that is compatible with MNI space in FSL. I was planning on extracting CC labels and then converting the labels from fsaverage space to MNI space. I first tried to extract the 5 separate CC labels using the command: mri_vol2label --c aparc+aseg.mgz --id 255 --l 255.label. When viewed in FreeView, the labels were spotty looking. Did I do this mgz to label extraction correctly? [cid:7dee544f-74a8-43d0-be89-9af1a0c74e2f] And also do you have a recommended code to convert FreeSurfer CC subregions into MNI space ROIs for FSL? Best, Jessica

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recon-all errors after mri_pretess
by Alexopoulos, Dimitrios 17 Mar '22

17 Mar '22

External Email - Use Caution Hi, we're running FS 7.2 'recon-all -all' on a subject and are getting errors on our cluster (CentOS 8) The attached recon-all.log file is attached for details. The last several lines of the file are below. Any comments as to why its failing? Jim. pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 631 (out of 421942: 0.149547) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2022:03:03:12:51:58 mri_pretess N 4 e 3.84 S 0.01 U 3.70 P 96% M 56636 F 1 R 2214 W 0 c 330 w 325 I 8801 O 646 L 3.37 3.47 3.45 @#@FSLOADPOST 2022:03:03:12:52:02 mri_pretess N 4 3.37 3.47 3.45 #-------------------------------------------- #@# Fill Thu Mar 3 12:52:02 CST 2022 ________________________________ 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.

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Using vol2surf to fsaverage.
by Jacoby, John 17 Mar '22

17 Mar '22

Hi all, Usually when I want to map volume data to the fsaverage surface, I use mri_vol2surf with a registration that transforms the volume into the space of the subject's orig.mgz and with --trgsubject set to 'fsaverage'. Currently, I have some volumes that have already been transformed to the subjects' orig.mgz space that I want to bring to the fsaverage surface. Can I still just give mri_vol2surf the same registration that I used to transform this volume in the first place, or will this try to re-apply that registration and end up in the wrong space? If that's incorrect, what's the best way to go about doing this? Thank you! Best, John

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FWHM errors for mri_glmfit-sim for lgi?
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 17 Mar '22

17 Mar '22

External Email - Use Caution I receive FWHM values much larger than what average/mult-comp-cor/fsaverage/rh/cortex has (around ~50) w/ LGI, but normal when looking at GM thickness. Is this expected? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Re: [Freesurfer] Freesurfer Digest, Vol 217, Issue 29
by Goeckner, Bryna 17 Mar '22

17 Mar '22

External Email - Use Caution Anastasia, Thanks for your help on this! I looked through the subjects for which the corticospinal tract failed, and the scans didn’t seem truncated compared to the ones that ran successfully. But since we are not particularly concerned with the cst, I thought I’d try to run all other pathways. Based on info for setting up the config file, I thought adding this line to the config file would work: set pathlist = ( acomm cc.bodyc cc.bodypf cc.bodypm cc.bodyp cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af lh.ar lh.atr lh.cbd lh.cbv lh.emc lh.fat lh.fx lh.ilf lh.mlf lf.or lh.slf1 lh.sl2 lh.slf3 lh.uf rh.af rh.ar rh.atr rh.cbd rh.cbv rh.emc rh.fat rh.fx rh.ilf rh.mlf rh.or rh.slf1 rh.slf2 rh.slf3 rh.uf ) But I got this error message: ERROR: length of pathway list (acomm cc.bodyc cc.bodypf cc.bodypm cc.bodyp cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af lh.ar lh.atr lh.cbd lh.cbv lh.emc lh.fat lh.fx lh.ilf lh.mlf lf.or lh.slf1 lh.sl2 lh.slf3 lh.uf rh.af rh.ar rh.atr rh.cbd rh.cbv rh.emc rh.fat rh.fx rh.ilf rh.mlf rh.or rh.slf1 rh.slf2 rh.slf3 rh.uf) and endpoint label ID list ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 10 0 0 0 0 28 0 0 0 0 0 0 49 49 0 0 0 0 60 0 0 49 0 0 0 0) do not match Looks like I need to change the endpoint label ID list? How would I do that? Bryna Goeckner (she/her) Graduate Student Medical College of Wisconsin Neuroscience Doctoral Program Date: Thu, 17 Mar 2022 18:18:26 +0000 From: "Yendiki, Anastasia" <AYENDIKI(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Reposting TRACULA trac-all -prep finishes with errors To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MN2PR04MB681631333C83A03772141E4B8A129(a)MN2PR04MB6816.namprd04.prod.outlook.com> Content-Type: text/plain; charset="windows-1252" Hi Bryna - I see that the error occurs in the corticospinal tract. Any change the top or bottom of the brain is truncated in this subject's scan? Anastasia. ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Goeckner, Bryna <bgoeckner(a)mcw.edu> Sent: Thursday, March 17, 2022 11:53 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Reposting TRACULA trac-all -prep finishes with errors External Email - Use Caution Attaching config file & link to trac-all.log (trac-all/log is kind of big ? so freesurfer listserv blocked email). Hopefully you are able to access them this way. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1pFVh-66Hoz8ai7X8JA6lojOQYdcauq9l7ExKYgOe8pXrh…<https://secure-web.cisco.com/1NOZCdcgx_oUa395czxw_g_-1lzisZMf2N17J7ReicSYgO…> <https://secure-web.cisco.com/1TJ2tok7mbzdMdCHQyHMjDCCmd4IqA_r-HGdAkeg6_NrmO… > From: Goeckner, Bryna <bgoeckner(a)mcw.edu> Date: Monday, February 14, 2022 at 4:42 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: TRACULA trac-all -prep finishes with errors Hi FreeSurfer Developers, I am attempting to run data for several subjects through TRACULA using trac-all -prep, but some of them have finished with errors. I have checked registration for all of them and it looks ok. I am including a link to my confi

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Advanced fMRI Applications Postdoctoral Fellow Position at Carle Health
by Yendiki, Anastasia 17 Mar '22

17 Mar '22

Passing along this opening at the Carle Illinois Advanced Imaging Center on behalf of Dr. Sheeba Arnold Anteraper: https://www.ismrm.org/jobs/j07799.pdf Anastasia.

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Trac-all -prep -c error
by Kaplan, Elizabeth 17 Mar '22

17 Mar '22

External Email - Use Caution Hello All, I am attempting to process images using tracula, however I am running into an error when attempting to run the "trac-all -prep -c" command line. Parcellation was ran on FS 7.2.0, However, I am running the command on freesurfer dev version due to an earlier resolved error reading index file: https://secure-web.cisco.com/1NrhFqWiJIFbTxyFpNb7jAq78TXhI1EKDKQf_a4RRwqAAO… Trac-all exits on the command: CMD mri_binarize --i /autofs/cluster/lazar/Projects/DTIanalysis/Subjects_DTI_t1t2/AG010_1308_T1_LAZAR_recon.long.AG010_1308/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /autofs/cluster/lazar/Projects/DTIanalysis/Subjects_DTI_t1t2/AG010_1308_T1_LAZAR_recon.long.AG010_1308/dlabel/anatorig/aparc+aseg_mask.nii.gz The Trac-all.log reads "mri_binarize done", see attached, and the outputs from the mri_binarize command are present. I used the longitudinal configuration file example on the wiki, attached below. Any guidance on how to navigate the issue would be greatly appreciated! Thank you!

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Re: [Freesurfer] Reposting TRACULA trac-all -prep finishes with errors
by Goeckner, Bryna 17 Mar '22

17 Mar '22

External Email - Use Caution Attaching config file & link to trac-all.log (trac-all/log is kind of big – so freesurfer listserv blocked email). Hopefully you are able to access them this way. https://secure-web.cisco.com/12mEXYhuUBlTXDgjHzPTswpMwBUz25h_vFGE_6-rakbDLz… From: Goeckner, Bryna <bgoeckner(a)mcw.edu> Date: Monday, February 14, 2022 at 4:42 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: TRACULA trac-all -prep finishes with errors Hi FreeSurfer Developers, I am attempting to run data for several subjects through TRACULA using trac-all -prep, but some of them have finished with errors. I have checked registration for all of them and it looks ok. I am including a link to my config file, and the trac-all.log and trac-all.error files for one subject: https://secure-web.cisco.com/12G4PlLvcpklUuTh8D_a28ezMniUQvE-KhDPzm3bm138_O… FreeSurfer version: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b Any help you can give me is greatly appreciated. Thanks! Bryna Goeckner (she/her) Graduate Student Medical College of Wisconsin Neuroscience Doctoral Program

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error with trac-all -prep in FS7.2 tracula
by Alexopoulos, Dimitrios 17 Mar '22

17 Mar '22

External Email - Use Caution Hi all, We are reprocessing some of our data with FS 7.2 to evaluate the new updates to Tracula, however, we are getting errors from the trac-all -prep -c configfile step. The last 20 lines of output are shown below. Anyone have any comments on how to correct this? ------------------------------------- trac-preproc exited with ERRORS at Fri Feb 11 18:18:29 CST 2022lines: 1DIAGNOSTIC, 24, -4.743908838687e-01, 5.860622007851e-05, 4.2190e+01, 1.4997e+00, 1DIAGNOSTIC, 25, -4.743823138430e-01, 4.831431802083e-05, 4.3721e+01, 1.5312e+00, 1DIAGNOSTIC, 26, -4.744830990496e-01, 3.946018283887e-05, 4.5293e+01, 1.5718e+00, 1DIAGNOSTIC, 27, -4.744857576549e-01, 3.343839305766e-05, 4.6879e+01, 1.5857e+00, 1DIAGNOSTIC, 28, -4.744568952592e-01, 2.896457797682e-05, 4.8446e+01, 1.5669e+00, 1DIAGNOSTIC, 29, -4.744930355970e-01, 2.351784987169e-05, 5.0045e+01, 1.5996e+00, 1DIAGNOSTIC, 30, -4.744428763349e-01, 1.764564796251e-05, 5.1621e+01, 1.5762e+00, 1DIAGNOSTIC, 31, -4.744390742695e-01, 1.211632175497e-05, 5.3234e+01, 1.6130e+00, 1DIAGNOSTIC, 32, -4.744465209349e-01, 6.742111363235e-06, 5.4833e+01, 1.5989e+00, 1DIAGNOSTIC, 33, -4.743750058790e-01, 8.816157837238e-07, 5.6420e+01, 1.5867e+00, Elapsed time (stage 2): 58.59 Total elapsed time: 71.08 ConvertTransformFile 3 /data/shimony/shimony2/neonatal/wunder_9_10yo/freesurfer7.2/neo289e/dmri/xfms/diff2syn0GenericAffine.mat /data/shimony/shimony2/neonatal/wunder_9_10yo/freesurfer7.2/neo289e/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux hopper 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux That piece of code is part of the ANTS library. When I look at the code this is what I see (or don't see for that matter) # Register FA nonlinearly to FA template with SyN set cmd = $ANTSPATH/antsRegistrationSyNQuick.sh <-- This ANTs code has $ANTSPATH set cmd = ($cmd -d 3) set cmd = ($cmd -m $dwidir/dtifit_FA.nii.gz) set cmd = ($cmd -f $intertrg) set cmd = ($cmd -o $xfmdir/diff2syn) echo $cmd |& tee -a $LF |& tee -a $CF if ($RunIt) then $cmd |& tee -a $LF if ($status) goto error_exit endif # Convert affine transform to .lta set cmd = ConvertTransformFile <-- This ANTs code DOES NOT have $ANTSPATH ________________________________ 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.

2 2

TRACULA trac-all -prep finishes with errors
by Goeckner, Bryna 17 Mar '22

17 Mar '22

External Email - Use Caution Hi FreeSurfer Developers, I am attempting to run data for several subjects through TRACULA using trac-all -prep, but some of them have finished with errors. I have checked registration for all of them and it looks ok. I am including a link to my config file, and the trac-all.log and trac-all.error files for one subject: https://secure-web.cisco.com/1fMOW2H4XkhFM0lHgtKrt25eEfHZNAPKOFCoBf2ppUW5T2… FreeSurfer version: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b Any help you can give me is greatly appreciated. Thanks! Bryna Goeckner (she/her) Graduate Student Medical College of Wisconsin Neuroscience Doctoral Program

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