Freesurfer

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19 participants
30088 discussions

Yeo Atlas Download
by Aster, Hans-Christoph 15 Jun '19

15 Jun '19

External Email - Use Caution Dear Freesurfer Team, I cannot download the "Resting State Cortical Parcellation in nonlin MNI152 space" with several machines. Is there something wrong with the server? The error message is: Server Connection was reset. Thank you in advance, kind regards Hans --- Dr. med. univ. Hans-Christoph Aster Neurologische Klinik Universitätsklinikum Würzburg Josef-Schneider-Str. 11 D-97080 Würzburg Tel. +49 931 201 23668 Aster_H(a)ukw.de<mailto:Aster_H@ukw.de> http://www.neurologie.ukw.de/

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fsaverage error with recon-all
by chen 14 Jun '19

14 Jun '19

External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set. Batching exited with an error indicating there is not fsaverage/surf/lh.sphere.reg. I was able to run a subject before without any error not sure why all the subjects I ran now over the weekend ended up with same error. The detail information please see the attachments.Thanks in advance.Jiachen ------------------

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incompatible vertex number ???
by Barletta, Valeria 14 Jun '19

14 Jun '19

Dear Freesurfers, I am getting this type of error in the Terminal when I open my images on Freesurfer: MRISreadNewCurvature: incompatible vertex number in file /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSTAT_MS_001_B/surf/lh.curv No such file or directory could not read curvature from curv No such file or directory mpatible vertex number in file /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSTAT_MS_001_B/surf/lh.curv I can still visualize and modify the images, but I noticed that recon-all autorecon2-wm for wm edits is not working. Are these two things related? Thank you, Vale

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Cannot convert mgz to nii
by Ritesh Mahajan 14 Jun '19

14 Jun '19

External Email - Use Caution Hello Team, I was working on mind boggle data set. I downloaded the freesurfer results from "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/HM…" I am unable to convert aseg.mgz to aseg.nii for HLN group. Please note that i was able to convert all other groups(MMRR, NKI-TRT, NKI-RS). Command i tried "mri_convert aseg.mgz to aseg.nii" it throws cannot allocate memory error, where as it works for all other series other than HLN. I have attached the screen shot of error message for your reference. Can you please help me out? Thanks, RItesh Mahajan

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Recon-all taking 20 hours to run.
by Aaron Tanenbaum 13 Jun '19

13 Jun '19

External Email - Use Caution I ran 38 subjects through Freesurfer 6.0 on a supercomputer here at Washu. The super computer is about 3 years old. Of those 38 subjects, 7 exceeded 20 hour time limit on the batch script. The others took about 12 hours to finish. All subjects had a 1mm isotropic MPRAGE and FLAIR. Below is the command I used for one of them. Is there a reason for some subjects recon-all would take more then 20 hours? recon-all -s 100000016_20170414 -i /scratch/brierm/Images/100000016_20170414_T1.nii -FLAIR /scratch/brierm/Images/100000016_20170414_FLAIR.nii -FLAIRpial -all -mprage -hippocampal-subfields-T1 -qcache

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Re: [Freesurfer] Tksurfer and qdec: error sourcing and floating exception
by fsbuild 12 Jun '19

12 Jun '19

External Email - Use Caution Hello Wafaa, I believe qdec runs as a 32 bit application.  You may see Mac OS 10.14 put up a window warning that an application is not optimized for the system and needs to be re-compiled by its developer; that means it is a 32 bit app.  While many 32 bit apps that ran on High Sierra (10.13) run on Mojave (10.14), I don't think it is guaranteed they will run OK on 10.14, e.g., qdec trying to use 32 bit floats while Mac OS 10.14 is expecting apps to use 64 bit floats.  I do know that 32 bit apps will not run at all on the next rev of Mac OS that was just announced, Catalina, Mac OS 10.15.  I don't know if there is a 64 bit version of qdec. - R. Wafaa Sweidan June 12, 2019 at 12:54         External Email - Use Caution         Hello all, I have been using freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c on macos high sierra, then I updated to mojave 10.14. freeusrfer was working all good for a while. BUT, for unknown reasons, I am no longer able to overlay the significance maps using tksurfer and cant open qdec, like below: command: tksurfer fsaverage lh inflated output error: subject is fsaverage hemi    is lh surface is inflated surfer: current subjects dir: /Users/wsweidan/Desktop/GLM_trial surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer:     /Users/wsweidan/Desktop/GLM_trial checking for nofix files in 'inflated' Reading image info (/Users/wsweidan/Desktop/GLM_trial/fsaverage) Reading /Users/wsweidan/Desktop/GLM_trial/fsaverage/mri/orig.mgz surfer: Reading header info from /Users/wsweidan/Desktop/GLM_trial/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: single buffered window surfer: tkoInitWindow(fsaverage) setting percentile thresholds (-1.00, 0.00, 0.00) surfer: using interface /Applications/freesurfer/tktools/tksurfer.tcl Reading /Applications/freesurfer/tktools/tkm_common.tcl Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/tktools/tkUtils.tcl Error sourcing /Applications/freesurfer/tktools/tksurfer.tcl: bad distance "0.125i": can't be negative reading white matter vertex locations.... % Floating exception command: qdec output error: Floating exception I reinstalled freesurfer again and I still get the same errors. Freeview works just fine. Any input of how to solve this issue?  Thanks in advance,  Wafaa _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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multi-slice timing correction
by Joseph Dien 12 Jun '19

12 Jun '19

External Email - Use Caution Hi Doug, I’m happy to see that FreeSurfer6 provides enhanced support for slice timing. I’m trying to run it on some multi-slice data. May I ask you for some guidance on how to use the new preproc-sess options? As I understand it, I would specify “-ngroups 10” because the data were collected in ten groups of six slices at a time? I’m not sure how to specify “-sliceorder”. Slice times are below. Thanks for any help you can provide. Joe 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.com

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Re: [Freesurfer] hippocampal subfield as CONN seeds
by Nelson, Eric A 12 Jun '19

12 Jun '19

External Email - Use Caution Im not sure I understand the question because I have not successfully registered the hippoSfLabels file to mni space. I can load the hippoSfLabels.mgz file into CONN at the subject level, but I have two problems. 1st it is not in MNI space. 2nd it is the whole hippocampus and I want to be able to use masks of the individual subfields. To try and convert the hippoSfLabels file to MNI space though I used the following. mri_vol2vol --mov lh.hippoSfLabels-T1-T2.v10.mgz \ --targ $FREESURFER_HOME/average/mni305.cor.mgz \ --xfm transforms/talairach.xfm \ --o test.mgz Eric

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Problem with lme_mass_fit_vw
by Hua, Jessica 12 Jun '19

12 Jun '19

External Email - Use Caution Dear Kersten, Thank you so much for your help! I made a duplicate copy of the matlab directory, and the scripts worked perfectly. I had one quick question regarding the CM.C. Based on the Linear Mixed Effects model page, I modified the CM.C to fit my research question. I am interested in looking at change over time with BAC. If this is my model: Yij = ß1 + ß2*tij +ß3*adjBACi + ß4*adjBACi*tij + ß5*sexi + ß6*ICVi + b1i + b2i*tij + eij Would this be my CM.C?: [0 0 0 1 0 0] Just wanted to make sure that I was understanding the CM.C correctly. Best, Jessica Hua

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mri_gtmpvc with amended aparc+aseg
by Albrecht, Daniel S. 11 Jun '19

11 Jun '19

Hello, I’ve been using PETSurfer for partial volume correction of PET images using the RBV option. I’m amending the parcellations/segmentations to add in extracortical areas of high PET signal (to prevent spill-in into the brain), and after adjusting the *ctab file this runs successfully. However, I noticed the output resolution of the rbv.nii.gz image is the same as the input segmentation mask, not the expected 0.5mm iso. I’ve run a test incorporating the --rbv-res 0.5mm flag into the command line. The output rbv.nii.gz image is similar to the previous one (without the –rbv-res flag), again not as smooth as the typical output image. Is it satisfactory to run the command with my amended seg image and the --rbv-res 0.5mm flag, and are there any additional recommendations for running PVC with an amended seg image? Thanks very much, Dan

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