Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Error
by Weerasekera, Akila 23 Dec '20

23 Dec '20

Hello, I sent a few jobs to launchpad (FreeSurfer segmentation) and they exited with an exit=1, this is the error: "ERROR: Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version" I switched from Fs 6 to FS 7.1.1, how do I change the fsaverage link? Any help is appreciated. Thank you Akila Weerasekera, PhD | Postdoctoral Research Fellow Pain and Neuroinflammation Imaging Laboratory | Ratai Lab for Clinical Spectroscopy | Harvard Medical School | A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129 Mobile: (781) 820 4501 aweerasekera(a)mgh.harvard.edu <mailto:aweerasekera@mgh.harvard.edu> www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu> https://scholar.harvard.edu/loggia

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recon labels.DKT31.manual.nii.gz appears ERROR: Talairach failed
by 1248742467 23 Dec '20

23 Dec '20

External Email - Use Caution Hello, everyone I have download the labels.DKT31.manual.nii.gz in mindboggle datsets, I want to use recon-all command to get lh.labels.DKT31.manual.annot. But, when I run: recon-all -i labels.DKT31.manual.nii.gz -s bert5 -all, appears ERROR: Talairach failed ------------------------------ SUBJECT bert5 DATE Tue Dec 22 19:49:07 CST 2020 USER tj HOST bme01 PROCESSOR x86_64 OS Linux Linux bme01 4.15.0-123-generic #126-Ubuntu SMP Wed Oct 21 09:40:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ /home/tj/application/freesurfer/bin/recon-all PWD /home/tj/application/freesurfer/subjects/bert5/mri CMD talairach_afd -T 0.005 -xfm transforms/talairach.xfm

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Error with command: mri_em_register: RB40_talairach_2005-07-20.gca. No such file or directory
by Camerino, I.L. (Ileana) 23 Dec '20

23 Dec '20

External Email - Use Caution Dear Freesurfer experts, As indicated here https://secure-web.cisco.com/1U4b2EkUfPD8P1X6LdxE7H-WrQG5N2w5Lnh1FY6jUHMlzI… I am rerunning the code below to creare the file norm.mgz: mri_em_register -mask brain.mgz -p .5 nu.mgz \ $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca \ transforms/talairach.lta I got this error: == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/6.0/average/RB40_talairach_2005-07-20.gca'... GCAread(/opt/freesurfer/6.0/average/RB40_talairach_2005-07-20.gca): could not open file No such file or directory mri_em_register: could not open GCA /opt/freesurfer/6.0/average/RB40_talairach_2005-07-20.gca. No such file or directory This solution above does not work for me because the file : RB40_talairach_2005-07-20.gca does not exist in /opt/freesurfer/6.0/average I thought maybe the problem is that the file RB40_talairach_2005-07-20.gca is called now in a different way? Please could you tell me how the file “RB40_talairach_2005-07-20.gca” is called for Freesurfer v 6.0? there are two files in the folder “average” that terminate with .gca: RB_all_2016-05-10.vc700.gca or RB_all_withskull_2016-05-10.vc700.gca Thank you very much in advance Best regards Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618

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No extracerebral CSF in sGTM
by Julie Ottoy 23 Dec '20

23 Dec '20

External Email - Use Caution Dear Petsurfer team Does the sGTM PVC correct for the uptake in extra cerebral CSF? If not, how would this affect the reliability of the cortical PVC measures, considering the spill-out of grey matter uptake to csf is being ignored? Thank you! Best regards Julie

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cluster size and FWER rough equivalence?
by Kayle Sawyer 23 Dec '20

23 Dec '20

External Email - Use Caution We are working on a manuscript revision for an fMRI project that was analyzed with FS-FAST 5.3 years ago. We used mri_glmfit, and then we ran mri_surfcluster (instead of mri_glmfit-sim) with a vertex-wise threshold of p<0.001 and a cluster threshold of 100mm^2. We had applied 8 mm smoothing at the group-level, and the voxel size was 3.125x3.125x5 (resampled to fsaverage surface and to MNI305). 1. One reviewer asked us to provide a rough estimate of the family-wise error rate (FWER) that a cluster threshold of 100mm^2 is equivalent to, or alternatively, to re-analyze everything with mri_glmfit-sim permutation. It would be simpler to provide the FWER estimate. To get the FWER estimate, we referred to Woo et al (2014). However, their simulations were for volume analyses, not surface analyses. What is the FWER (roughly) for a primary threshold of p<0.001 and cluster threshold of 100mm^2? (Obviously, we are hoping for a number less than 0.05.) 2. For the volume, we used mri_surfcluster with a primary (voxel-wise) threshold of 0.001 and a size threshold of 300mm^3. If I’m understanding correctly, Figure 2 from Woo et al. (2014) suggests a FWER p<0.05 might roughly correspond to a cluster size threshold of 200 to 985 voxels (1600 to 7880 mm^3), depending on intrinsic smoothness. That would likely put our threshold of 300mm^3 well above p<0.05. Is this correct? Thanks, -Kayle

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Talairach Failure in recon-subject {Disarmed}
by Wei Shao 23 Dec '20

23 Dec '20

External Email - Use Caution Hi, Freesurfer team I have met a Talairach Failure problem when running the recon -all for a subject, here is the feedback: I tried -notal-check flag, but it might cause another problem when I use segmentHA_T2.sh to do hippocampus subfield segmentation. So, Could you help me to solve this problem? Thanks. #-------------------------------------------- #@# Talairach Failure Detection Mon Dec 21 17:59:09 EST 2020 /scratch/weishao/20191017_BAY10224/sub-BAY10224_Negar/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) @#@FSTIME 2020:12:21:17:59:09 talairach_afd N 4 e 0.07 S 0.01 U 0.00 P 18% M 6672 F 0 R 2777 W 0 c 2 w 65 I 1504 O 0 L 12.75 18.35 27.51 @#@FSLOADPOST 2020:12:21:17:59:09 talairach_afd N 4 12.75 18.35 27.51 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://secure-web.cisco.com/1_6NU0uyplJn2Ny1P23HKLCy4v6xjIjGaWl1oZJY8FTyZ1f… ERROR: Talairach failed! Linux gra824 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 GNU/Linux recon-all -s sub-BAY10224_Negar exited with ERRORS at Mon Dec 21 17:59:09 EST 2020 Best, Wei :

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Vertex-wise functional ROI extraction
by Sussman, Lauren 23 Dec '20

23 Dec '20

External Email - Use Caution Hello! I would like to extract functional data from a manually created label ROI on the surface on a vertex-wise basis. Funcroi-table-sess appears to only provide averaged values and I would like the value per vertex inside the ROI for the given contrasts. Is there a way to grab this data using Freesurfer? Thank you! Lauren

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Re: [Freesurfer] PFC segmentation
by Kothapalli, Satya 23 Dec '20

23 Dec '20

External Email - Use Caution Dear experts, Does anyone know how to extract the Prefrontal cortex region from the wmparc.mgz or aparc+aseg.mgz? Thanks, Satya. ________________________________ 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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fspalm contrasts {Disarmed}
by Marina Fernández 23 Dec '20

23 Dec '20

External Email - Use Caution Dear experts, To correct multiple comparisons on the surface I'm using fspalm. I know that this command internally transforms the design contrast and desing matrix from the Freesurfer format to the fsl format so that FSL-PALM understands the input. When the freesurfer contrasts include only one line, I can run permutations with fspalm without errors. The problem arises when the contrast has two lines (e.g., when including a three-level factor like in the example "Contrast 4: group.effect.mtx" from the link https://secure-web.cisco.com/1zRPseSPjbEGgbMXbZRKYmGKkEKOP342L-FeUKM_km6ilB…; or when including a two-way interaction between a dichotomic factor and two covariates of interest). You can see below the error. How can I solve this problem? Thank you in advance. Marina **ERROR:** Loading surface 1/1: /usr/local/freesurfer/subjects/amyloid74_thickness_average/surf/lh.white Reading input 1/1: /usr/local/freesurfer/subjects/amyloid74_thickness_stats/smoothing/gaussians/lh.fsgd_subj_gauss003.mgh Reading design matrix and contrasts. Error using palm_vestread (line 56) File not in the correct format: design.con Error in palm_miscread (line 110) [X.data,X.extra.PPH] = palm_vestread(X.filename); Error in palm_takeargs (line 2111) tmp = palm_miscread(opts.t{t},[],[],opts.precision); Error in palm_core (line 33) [opts,plm] = palm_takeargs(varargin{:}); Error in palm (line 81) palm_core(varargin{:});

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how to use recon-all command
by 1248742467 23 Dec '20

23 Dec '20

External Email - Use Caution Hello, everyone my freesurfer enviroment: Last login: Mon Dec 21 16:45:53 2020 from 10.16.10.109 -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /home/tj/application/freesurfer FSFAST_HOME       /home/tj/application/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /home/tj/application/freesurfer/subjects cd /home/tj/application/freesurfer/subjects MNI_DIR           /home/tj/application/freesurfer/mni I have a T1.nii.gz file, So where should I put this file in?  What's more, if I want to the output is in the input data file, how to set the recon-all command?

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Freesurfer