Freesurfer May 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
208 discussions

TRACULA prep roc error
by Batra, Vinita R. 04 May '20

04 May '20

External Email - Use Caution Hello team, I have encountered the following error while running the tracula pre-processing command and was hoping you could help me understand how to correct this. #@# Image corrections Sat May 2 19:57:18 CDT 2020 mri_convert --bvec-voxel /Users/sunlab/Documents/FreeSurferDirs/subjects_109_data/ /Users/sunlab/Documents/FreeSurferDirs/subjects_109//dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Users/sunlab/Documents/FreeSurferDirs/subjects_109_data/ /Users/sunlab/Documents/FreeSurferDirs/subjects_109//dmri/dwi_orig.nii.gz corRead(): can't open file /Users/sunlab/Documents/FreeSurferDirs/subjects_109_data/COR-.info $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/sunlab/Documents/FreeSurferDirs/subjects_109_data/... Darwin Suns-iMac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Oct 10 23:06:14 PDT 2018; root:xnu-4570.71.13~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Sat May 2 19:57:18 CDT 2020 Thank you, Vinita Batra

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PhD position at Lund University
by Laura Wisse 04 May '20

04 May '20

External Email - Use Caution Dear all, We have a PhD position available on imaging of the medial temporal lobe in aging and dementia at Lund University, Sweden, with the Biofinder Group. See here for more details and applying: https://lu.varbi.com/en/what:job/jobID:331266 The application deadline is June 7. Best, Laura Wisse

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error while obtaining lGI
by Yana Hoboken 04 May '20

04 May '20

External Email - Use Caution Dear Community, I am new to the software, so please bare with my ignorance! I have a triangular meshes of both hemispheres that were created not in FS but in another mesh generating software. I converted them with nibabel into two .pial files. When I run a 'read' command on them, I see the same structure as I see on native .pial file: [image: image.png] Previously I have already run a recon-all on the MRI data I have and generated lh/rh.pial files. I also run -localGI on them, and also got the results just fine. Every time I work on the same computer. THe meshes that I converted with nibabel look the same (except for transcription) as the one I got from MRI. I cannot distinguish them in Freeview. But when I try to get lGI I got the error message. The command I use : recon-all -s name -localGI THe error I got: I will attached the log file for more information. FS version I am using: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c I will be very grateful for any tips what this error is about, as I cannot find any reference about it anywhere. Thank you for you time! Yana

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Re: [Freesurfer] Freesurfer Digest, Vol 194, Issue 45
by atira gan-zvi bick 03 May '20

03 May '20

External Email - Use Caution Hi Bruce > It worked! how simple... Thank you so much. Atira > > > ------------------------------ > > Message: 2 > Date: Sun, 26 Apr 2020 12:04:36 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] exporting segmented mgz file > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.2004261203210.6647(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Atira > > what was your mri_convert command line? Make sure to specify no scaling of > the intensity volume. Can you try adding: > > -ns 1 > > to the mri_convert command line, and if that doesn't work send us the full > command line and full screen output from it? This is always a good thing > to > do as it gives us enough information to help > > cheers > Bruce > > > > On Sun, 26 Apr 2020, atira gan-zvi bick wrote: > > > > > ????????External Email - Use Caution???????? > > > > Hi > > I'm new to freesurfer. > > > > I used freesurfer to preform Thalamus segmentation, and can see the > segmented?volume in freeview. > > I would like to export?the segmented volume to nii to continue analysis > in MRvista. > > I was able to do this using?mri_convert - however the values in the > nifti are not those on the label > > list (as seen in ?freeview). The number of different values is similar > but not the same, and the values > > themselves? are totally different?(8103-8233 in freeview, 16384 - > 32767). It is possible to compare > > regions based on visual inspection - however that is tedious?and might > lead to mistakes. > > How can I export the labels of each region in the segmented mgz? > > > > Any suggestions? > > I'd appreciate?to learn fro your experience > > > > Thanks > > Atira > > > > -- > > ?"? ????? ??-??? ??? > > ????? ?????? ???????? > > ???? ???-??? > > ??????????? ?????? > > > > Atira Bick (Phd) > > fMRI unit > > Hadassah medical center, Hebrew University > > Jerusalem > > > > > > ------------------------------ > > > > -- ד"ר עתירה גן-צבי ביק יחידת ההדמיה התפקודית הדסה עין-כרם האוניברסיטה העברית Atira Bick (Phd) fMRI unit Hadassah medical center, Hebrew University Jerusalem

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Re: [Freesurfer] convert MNI152 coordinates into vertex index
by Marina Fernández 02 May '20

02 May '20

External Email - Use Caution Thank you for the information, Bruce and Thomas! Thomas, I think this utility is perfect! I tried it with fsaverage subject without problems. Do you think I can use this function to calculate the vertex of the fsaverage5 (instead of the fsaverage)? Really, thank you very much, this help is very useful for us! Best regards, Marina

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mri_glmfit
by jiahui 02 May '20

02 May '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare two groups' cortex, but for some of my subjects I get the following error when I run mri_glmfit \ --y rh.thickness.10.mgz \ --fsgd g3v1.fsgd dods\ --C group.mtx \ --surf fsaverage rh \ --cortex \ --glmdir g3v1.rh ERROR: DOF=0(this is error?) g3v1h.rh only 4 files(should have beta.mgh sig.mgz files...) I've searched the list and no similar errors have been reported. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: ubuntu 16.04.6 LTS 3) mri_glmfit.log and figure01 figure02 figure03: see attached

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To normalize fMRI data in MNI152 template
by Kim, Gwang-Won 02 May '20

02 May '20

Dear expert, I’ like to normalize fMRI data in MNI152 template. Is it right?: “preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -cvs -fwhm 5 -per-run” Thanks, Gwang-Won

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mri_glmfit
by jiahui 02 May '20

02 May '20

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Intensity inhomogeneity messing with the wm.mgz
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 02 May '20

02 May '20

Hi Freesurfer developers, I have a subsample of a FS dataset that have scanner-originated hyperintensities in the bilateral supramarginal/temporal lobes. I've manually removed these hyperintensities by editing the wm.mgz, yet FS seems to be unable to recognize these edits when looking at the ?h.white and aparc+aseg.mgz. Is there a possible way to rectify these errors? I am using FS6 for linux Here are some pictures: [cid:b4c23099-ffe0-4054-83b9-730a124b78e9]?[cid:35eb0541-c4de-4d31-9f85-4986e1e26661] Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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mri_glimfit error - help!
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 01 May '20

01 May '20

External Email - Use Caution Dear Freesurfer experts, I'm having a persistent error with mri_glimfit. The fsgd file isn't being read correctly, despite following the exact requirements of the wiki. Also, the output mentions this "carriage returns warning", and despite running this conversion: cat fsgd_file.fsgd | sed 's/\r/\n/g' > new.fsgd_file.fsgd, the *new fsgd still doesn't work* (this code somehow alters the Group Descriptor at the top of the file, giving another error). I've attached my fsgd file (that I used while running the code below) Also, please see the full error of the glim_fit below: WARNING: carriage returns have been detected in file fsgd_file.fsgd Was it created on a Windows computer? This may cause an error in reading the FSGD file. If so, try running: cat fsgd_file.fsgd | sed 's/\r/\n/g' > new.fsgd_file.fsgd Then use new.fsgd_file.fsgd INFO: ignoring tag Tile INFO: ignoring tag nput INFO: ignoring tag nput INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.839844 AvgVtxArea 0.396851 AvgVtxDist 0.717994 StdVtxDist 0.193566 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Applications/freesurfer/BAP/group_analysis_data/qdec cmdline mri_glmfit.bin --y fsgd_RH_thickness.mgh --fsgd fsgd_file.fsgd dods --C contrasts.mtx --surf fsaverage rh --glmdir rhBAP_thickness.glmdir sysname Darwin hostname CCASPH-A1900447.cloud.ccas.gwu.edu machine x86_64 user ajobsaid FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/BAP/group_analysis_data/qdec/fsgd_RH_thickness.mgh logyflag 0 usedti 0 FSGD fsgd_file.fsgd labelmask /Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/label/rh.cortex.label maskinv 0 glmdir rhBAP_thickness.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory rhBAP_thickness.glmdir Loading y from /Applications/freesurfer/BAP/group_analysis_data/qdec/fsgd_RH_thickness.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to rhBAP_thickness.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 1e+10 Design matrix ------------------ -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+10 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y fsgd_RH_thickness.mgh --fsgd fsgd_file.fsgd dods --C contrasts.mtx --surf fsaverage rh --glmdir rhBAP_thickness.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=99999997952.000000 (col 0), Max=0.000000 (col 0) ... could not determine the cause of the problem Thanks! Alex Job

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Freesurfer May 2020