Freesurfer April 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
170 discussions

(No Subject)
by KennethSPrice 11 May '20

11 May '20

External Email - Use Caution Hello Freesurfer friends! I'm going through the "paired analysis" tutorial and am running into an issue with the mri_glmfit. I am running on just one subject pair. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit I ran mris_preproc on my 2 timepoints and am getting an error at mri_glmfit mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff mri_glmfit \ --glmdir lh.paired-diff \ --y lh.paired-diff.thickness.sm05.mgh \ --fsgd paired-diff.fsgd \ --osgm \ --surf fsaverage lh I am getting an ERROR: DOF = 0. MRI's have been put through recon-all and are in there own directories within SUBJECTS_DIR. What is the cause of the error? Thanks, Ken Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as one of the nation’s top hospitals by U.S. News & World Report (2019-2020). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

2 5

Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors
by Zeng, Qi 04 May '20

04 May '20

External Email - Use Caution Hi Eugenio, Thank you so much for the prompt reply ! Here attached the log file. The files generated: SUBJ/SUBJ_base/tmp/hippoSF_T1_long.v21_left SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1 Best, Qi On Wed, Apr 29, 2020 at 5:22 PM Zeng, Qi <qi.zeng(a)icahn.mssm.edu> wrote: > Hi Eugenio, > > Thank you so much for the prompt reply ! > Here attached the output error and log file. > The files generated: > SUBJ/SUBJ_base/tmp/hippoSF_T1_long.v21_left > SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1 > > Best, > Qi > > On Wed, Apr 29, 2020 at 3:23 PM Iglesias Gonzalez, Juan E. < > JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: > >> Dear Qi, >> >> The correct syntax is that of your First try, but I’m very surprised you >> got that error, as we fixed this a while ago… Can you please send me the >> complete output? >> >> Cheers, >> >> /Eugenio >> >> >> >> >> >> Juan Eugenio Iglesias >> >> Senior research fellow >> >> CMIC (UCL), MGH (HMS) and CSAIL (MIT) >> >> http://www.jeiglesias.com >> >> >> >> >> >> >> >> *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" >> <qi.zeng(a)icahn.mssm.edu> >> *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> *Date: *Wednesday, April 29, 2020 at 04:44 >> *To: *"freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >> *Subject: *[Freesurfer] Longitudinal Hippocampal Subfields Module, >> existed with errors >> >> >> >> * External Email - Use Caution * >> >> Hi, >> >> I am trying to use the longitudinal pipeline of the “hippocampal >> subfields and nuclei of amygdala”. Keep getting error messages when running >> it longitudinal but with no error message running it cross-sectional. I >> want to know if there is any way to fix the error and to run a longitudinal >> pipeline successfully. >> >> I am using Freesurfer/dev and matlab_runtime/2014b. >> >> I got two timepoints for each subject and finished recon-all longitudinal >> with no errors. >> >> 1) First Try >> >> segmentHA_T1_long.sh SUBJ_base >> >> >> run for about 15 mins and exited with error message: >> >> “Error using kvlGEMSMatlab >> >> >> /autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/kvlAtlasMeshDeformationOptimizer.cxx:327: >> >> itk::ERROR: AtlasMeshDeformationLBFGSOptimizer(0x2ac1fead7740): search >> direction is not a descent direction! >> >> Error in kvlStepOptimizer (line 11) >> >> Error in SegmentSubfieldsT1Longitudinal” >> >> >> no mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21 >> generated. >> >> >> >> 2) Second Try >> >> segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_base >> >> segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_base >> >> >> run for about 16 mins, most successful but a few with errors: >> >> “Error in segmentSubjectT1_autoEstimateAlveusML (line 1539)” >> >> Or >> >> >> >> >> “Open file failed because file >> '/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m' >> has invalid content. Details: 'file is closed.failbit is set.' >> >> The file >> >> >> "/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m" >> >> cannot be executed. >> >> Error in segmentSubjectT1_autoEstimateAlveusML (line 538)” >> >> >> >> >> successful done subject or hemisphere generated >> mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21. >> >> >> >> 3) Third Try cross-sectional >> >> segmentHA_T1.sh SUBJ1_timepoint1 >> >> segmentHA_T1.sh SUBJ1_timepoint2 >> >> >> run for about 15 mins, all successful with no errors: >> >> >> all subjects have mri/lh.amygNucVolumes-T1.v21 and >> mri/lh.hippoSfVolumes-T1.v21 generated. >> >> >> >> Manual inspection with freeview, it seems fine with all successful >> longitudinal and cross sectional subfield segmentation outputs mgz. >> >> >> >> I wonder if I can fix first try and second try errors so that >> longitudinal output can be generated. >> >> >> >> Thank you for your help! >> >> Best, >> >> Qi >> >> >> >> -- >> >> >> >> Ph.D. candidate >> >> Icahn School of Medicine at Mount Sinai >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Ph.D. candidate > Icahn School of Medicine at Mount Sinai > > -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

2 13

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

2 1

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.

2 6

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

2 2

Ubuntu VM password
by Alex Mihai 01 May '20

01 May '20

External Email - Use Caution Hi guys! I have followed the virtual machine setup for virtual box freesurfer installation.but it ask me the password for the developer account. Which is the password? Cheers, Alex

2 1

trac-all -bedp error
by Zeng, Qi 30 Apr '20

30 Apr '20

External Email - Use Caution Hi, I run trac-all, the log file has the following endings. "Queuing post processing stage" or "Queuing post processing stage 59 slices processed All slices processed /hpc/packages/minerva-common/freesurfer/6.0.0/freesurfer/bin/bedpostx_mgh: line 345: kill: (100952) - No such process". However, all outputs described in FSL BedpostX are generated dmri/FA, MD, V1, V2, V3 dmri.bedpostX/merged,mean,dyads, nodif_brain_mask Should I consider them as completed and move forward with -path? Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

2 2

longitudinal dmrirc script error with the baselist
by Zeng, Qi 30 Apr '20

30 Apr '20

External Email - Use Caution Hi, I have my trac-all up and running with no error with individual subjects when I set the subject directory to individual subjects. as follow: set SUBJECTS_DIR=/*/subjects/SUBJ1 set subjlist = (SUBJ1_ses-1 SUBJ1_ses-2) set baselist = (SUBJ1_base SUBJ1_base) However, when I put subjects together and set the directory to multiple subjects as follow: set SUBJECTS_DIR=/*/subjects set subjlist = (SUBJ1/SUBJ1_ses-1 \ SUBJ1/SUBJ1_ses-2 \ SUBJ2/SUBJ2_ses-1 \ SUBJ2/SUBJ2_ses-2 \ etc. ) set baselist = (SUBJ1/SUBJ1_base \ SUBJ1/SUBJ1_base \ SUBJ2/SUBJ2_base \ SUBJ2/SUBJ2_base \ etc.) It has a problem finding the baselist file: "cannot find /*/subjects/SUBJ1/SUBJ1_ses-1.long.SUBJ1/SUBJ1_base". Should I copy SUJB1_base under the SUBJ1.long.SUBJ1 and run it again? Why is it not happening with the subject individual? Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

2 3

FreeSurfer 7 stable
by Mina Rizkallah 30 Apr '20

30 Apr '20

External Email - Use Caution Greetings FreeSurfer team, I have some questions regarding the latest stable version of freesurfer; 1- I am currently using Centos 8, and the Freesurfer download link for this version says centos 7 not 8.. is it compatible with centos 8? 2- Is it true that CUDA is no longer available for freesurfer? is there any other option for GPU acceleration? as it was crucial for recon-all speed (got 2.7 hours/subject instead of 6 hours on version 6). best regards Mina

1 0

FreeSurfer version 7.0.0 is now available
by Douglas N. Greve 30 Apr '20

30 Apr '20

We are pleased to announce the release of FreeSurfer version 7. You can get the new software from here https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall You can find the release notes here https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Let us know how it goes best doug and the FreeSurfer development team

1 0

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Freesurfer April 2020