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30132 discussions

Thalamic Nuclei segmentation results
by Dev vasu 09 Oct '18

09 Oct '18

External Email - Use Caution Dear all, I have used Freesurfer pipeline for Thalamic Nuclei segmentation, the results of segmentation appear to be very poor, i am annexing the results , please kindly review if there is any thing wrong with the segmentation results. Thanks Vasudev

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recon-all terminated in middle : continuing an analysis of an existing subject
by Dev vasu 09 Oct '18

09 Oct '18

External Email - Use Caution Dear all, I was trying to run recon-all, the pipeline terminated in middle now i would like to know if there is any way i can restart it from the point where it was terminated?. Thanks Vasudev

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nu_correct disk i/o issues
by Jasper van den Bosch 09 Oct '18

09 Oct '18

External Email - Use Caution We are trying to run recon_all inside an fmriprep singularity container, but are running into an issue with nu_correct. It says it cannot write to disk, however there is plenty of space on the tmpdir and output dir. Does this script try to write to any other locations? Because this would fail inside the container, where each writable location has to be 'mounted'. Error message: ncendef: ncid 5: No space left on device Error outputting volume: possibly disk full? nu_evaluate: crashed while running evaluate_field (termination status=139) nu_correct: crashed while running nu_evaluate (termination status=65280) ERROR: nu_correct Command ran: nu_correct -clobber ./tmp.mri_nu_correct.mni.1121/nu0.mnc ./tmp.mri_nu_correct.mni.1121/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1121/0/ -iterations 1000 -distance 50 [xxx@yyyy.cluster:/data/BIDS/derivatives/freesurfer/sub-1/mri/] [2018-10-04 14:59:29] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1121/0/ ./tmp.mri_nu_correct.mni.1121/nu0.mnc ./tmp.mri_nu_correct.mni.1121/nu1.imp this issue at the fmriprep repo: https://github.com/poldracklab/fmriprep/issues/1308 possibly related: https://github.com/freesurfer/freesurfer/issues/462 Many thanks for any advice, Jasper van den Bosch

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Extract individual vertex thickness values from cortical parcellations
by lindsay hanford 09 Oct '18

09 Oct '18

External Email - Use Caution Hello Freesurfer Community, I am looking for a way to extract thickness values at the level of each vertex from Freesurfer atlas-based parcellated regions (aparc.annot), or more generally lobes. Is this possible? Using mri_segstats I know it is possible to get more general metrics such as min, max and average thickness values, and # of voxels. Is it possible to use an annot file to read out the raw thickness values? This post was the closest I could find to answering my question, however, this was at the group level and not specified for parcellated regions. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022097.… Thank you in advance, Lindsay -- *Lindsay Hanford, PhD* *The Buckner Laboratory* *|* *Harvard University*

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very bad result using "mris_ca_train" and "mris_ca_label"
by Maedeh Khalilian 09 Oct '18

09 Oct '18

External Email - Use Caution Dear Dr.Bruce Fischl Thank you very much for your great sense of responsibility. Sure, i have sent you a zip file named "Maedeh_results"(it was a rather big sized one so i had to send it through Wetranser). Hope you have received it. However, a general question is that, according to freesurfer help the required arguments for "mris_ca_train" are : mris_ca_train [options] <hemi> <canon surf> <annot file> <subject 1> <subject 2> ... <output file> as it seems it gets one surf file(e.g sphere.reg),and one annotation file, but several subjects...so what does this surface file refer to?should i make an average of all subjects' .reg files? and also for the annotation file ! just one .annot is enough or i have to make an average of several annotation files? if yes, how should i do that? i would be grateful if you could help me. Best regards Maedeh,

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Talairach failed in monkey brain
by Frehiwot Woldeyes 09 Oct '18

09 Oct '18

External Email - Use Caution Hello Freesurfers, I was attempting to reconstruct a monkey brain, i encountered an error during talairach registration step, i have used tkregister2 to manually edit the registration but i have gotten error there too: tkregister2 --targ /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii --mov /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii --reg /usr/local/freesurfer/subjects/A004_crop.mhd.nii tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii movable volume /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii reg file /usr/local/freesurfer/subjects/A004_crop.mhd.nii LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 regio_read_register(): No such file or directory Could not open /usr/local/freesurfer/subjects/A004_crop.mhd.nii ERROR: reading /usr/local/freesurfer/subjects/A004_crop.mhd.nii Do you have any thoughts on how to troubleshoot this one? Regards, frehiwot

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m.khalilian@sutech.ac.ir sent you files via WeTransfer
by WeTransfer 09 Oct '18

09 Oct '18

External Email - Use Caution m.khalilian(a)sutech.ac.ir sent you some files 1 file, 378 MB in total ・ Will be deleted on 16 October, 2018 Download link: https://wetransfer.com/downloads/9370a847d04b46d6fcbc4faec24f094e2018100911… Message: Dear Dr.Bruce Fischl Thank you very much for your great sense of responsibility. Sure, i have attached a zip file named "Maedeh_results"(it was a rather big sized one so i had to send it through Wetranser). It contains my initial annotation files(as the input of 'mris_ca-train') by which i have made my atlas(?h.Desikan100.annot), my atlases for both hemispheres(?hDesikan100.gcs), a color LUT, my subject directory "test1" which i have used as the input of "mris_ca_train", another subject diectory "subj1", on which i have used to test my atlas, and finally my results "?h.finalDesikan100.annot" .(actually the result of applying my atlas on subj1) i myself guess that the main problem is that i am using just one subject as the input of "mris_ca_train", but i dunno how to get multiple subjects... that would be perfect if you could help me. Cheers Maedeh. 1 file Maedeh_results.zip [Get more out of WeTransfer, get Plus](https://wetransfer.com/plus?trk=WT201704_email&utm_campaign=WT_email_… About WeTransfer: https://wetransfer.com/about Help: https://wetransfer.zendesk.com/hc/en-us Legal: https://wetransfer.com/legal/terms To make sure our emails arrive, please add noreply(a)wetransfer.com to [your contacts](https://wetransfer.zendesk.com/hc/en-us/articles/204909429).

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Mri Convert Help
by Justin Arnett 08 Oct '18

08 Oct '18

External Email - Use Caution Hello Everyone, I hope you are doing well! I am trying to recon-all a DICOM file, for the ultimate hope of being able to identify the location of M1 via parcellation. I have successfully been able to do so for 2 subjects already, though for some reason I am having a problem with the MRI convert stage from the .dcm file to the .nii.gz file. I copied/pasted the terminal shell I tried performing above. I am using a Mac (Yosemite 10.10.5) with FreeSurfer V6.0.0 Further, I think it might be helpful to note that I am a very extreme novice in computer science/coding--I have completed recon-all's of 2 subjects by following, essentially line-by-line, the "FreeSurfer Download and Install Page," and this process was the first time I ever used the terminal shell. (In this way, I would absolutely LOVE if anyone might be able to explain where I went wrong as simplistically as possible). Thank you all so much for the help- I hope you have a great start to the week! - Justin DBI 05 MRI Convert Error Justins-Computer:~ justinarnett$ export FREESURFER_HOME=/Applications/freesurfer Justins-Computer:~ justinarnett$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects -bash: [: /Users/justinarnett: binary operator expected grep: /Users/justinarnett: Is a directory grep: 1/matlab/startup.m: No such file or directory grep: /Users/justinarnett: Is a directory grep: 1/matlab/startup.m: No such file or directory grep: /Users/justinarnett: Is a directory grep: 1/matlab/startup.m: No such file or directory MNI_DIR /Applications/freesurfer/mni Justins-Computer:~ justinarnett$ export SUBJECTS_DIR=/Applications/freesurfer/subjects/DBI05MRI Justins-Computer:~ justinarnett$ cd /Applications/freesurfer/subjects/DBI05MRI Justins-Computer:DBI05MRI justinarnett$ cp $FREESURFER_HOME/subjects/DBI05MRI/Image1.dcm usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directory Justins-Computer:DBI05MRI justinarnett$ mri_convert Image1.dcm Image1.nii.gz /Applications/freesurfer/FreeSurferEnv.sh: line 226: [: /Users/justinarnett: binary operator expected grep: /Users/justinarnett: Is a directory grep: 1/matlab/startup.m: No such file or directory grep: /Users/justinarnett: Is a directory grep: 1/matlab/startup.m: No such file or directory grep: /Users/justinarnett: Is a directory grep: 1/matlab/startup.m: No such file or directory mri_convert.bin Image1.dcm Image1.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from Image1.dcm... Starting DICOMRead2() dcmfile = /Applications/freesurfer/subjects/DBI05MRI/Image1.dcm dcmdir = /Applications/freesurfer/subjects/DBI05MRI Ref Series No = 401 Found 824 files, checking for dicoms WARNING: tag ImageNumber not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR WARNING: tag SeriesNumber not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR WARNING: tag image orientation not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR ERROR: GetDICOMInfo(): dcmGetDWIParams() 10 DICOM File: /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR break DICOMRead.c:5228 Found 164 dicom files in series. WARNING: tag ImageNumber not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR WARNING: tag SeriesNumber not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR WARNING: tag image orientation not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR ERROR: GetDICOMInfo(): dcmGetDWIParams() 10 DICOM File: /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR break DICOMRead.c:5228 First Sorting Computing Slice Direction Vs: -120.054 -103.192 34.4639 Vs: -0.741 -0.636922 0.212719 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 165 ndcmfiles = 165 MRIallocSequence(0, 0, 165, 1): bad parm No such file or directory ERROR: mri alloc failed

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FW: RE: error glm-fit-sim
by Caroline Beelen 08 Oct '18

08 Oct '18

External Email - Use Caution The command: gop@gop-linux:~/freesurfer$ freeview -f $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot -viewport 3d The output: reading colortable from annotation file... colortable with 1 entries read (originally none) colortable with 1 entries read (originally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) The command with a bit less strict significance level: gop@gop-linux:~/freesurfer$ freeview -f $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=3,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot -viewport 3d The output: reading colortable from annotation file... colortable with 1 entries read (originally none) colortable with 1 entries read (originally none) (and then it says no more). Both commands visualize the data, but no clusters are found. Is this how it should be? Does it mean that there is a problem with reading colortables or not? Best, Caroline Message: 2 Date: Mon, 1 Oct 2018 17:10:28 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> Subject: Re: [Freesurfer] error glm-fit-sim To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <504d6069-399f-163d-39a9-dcc6c02d32f9(a)mgh.harvard.edu<mailto:504d6069-399f-163d-39a9-dcc6c02d32f9@mgh.harvard.edu>> Content-Type: text/plain; charset="Windows-1252" What says that? What command are you running? What is the other terminal output? On 10/01/2018 04:54 AM, Caroline Beelen wrote: > > ????????External Email - Use Caution > > Dear FS, > > I followed the group analysis page for glm analysis and it worked fine > until the final step. I?m using version 5.3. After performing > glm-fit-sim it says ?glm-fit done? (for all files), but when trying to > open these it says: > > ?Reading colortable from annotation file? > > Colortable with 1 entries read (originally none) > > Colortable with 1 entries read (originally none) > > CTABisentryvalid: index -1 was 00B > > Resource temporarily unavailable > > CTABisentryvalid: index -1 was 00B > > Resource temporarily unavailable > > Resource temporarily unavailable? > > (etc..) > > It opens, but nothing is visible and I have the feeling it cannot open > color files?? > > MRI glmfit gives positive clusters for some values. I therefore used > the abs sign for glm-fit-sim. > > What might be wrong? > > Thanks. Caroline

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Difference between 6.0.1 and 6.0.0
by Haakon Ramsland Hol 08 Oct '18

08 Oct '18

External Email - Use Caution Dear Experts. I just happened to stumble across version 6.0.1, what is the main difference from 6.0.0? And I read in a post from 2017 that the flairpial wasn't optimized in v6.0.0 compared to 5.3, and that this would be optimized in version 6.1. Any news with regards to flair pial? Is it recommended to use 5.3 if you have flair images as well? Kind regards. Haakon R. Hol Radiologist.

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