Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

freesurfer segmentation: perirhinal Roi
by m.bahri＠uliege.be 08 Feb '18

08 Feb '18

Dear Freesurfer experts, We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin? Many thanks in advance, Best regards, -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Université de Liège - University of Liège GIGA-Cyclotron Research Centre: In Vivo Imaging, Bât B30, Quartier Agora Allée du six Aout n°8 4000 Liège, Belgium m.bahri(a)uliege.be Tel : + 32-4-3662304

3 12

Using subject specific template, atlas, & TPM
by Ramesh Babu 06 Feb '18

06 Feb '18

Dear experts, I have analysed T1 data using Freesurfer. Now we have created atlas, template & tissue probability map using different methods and softwares. I need your help to use template in freesufer, so that we can compare with default template and our template. Please help me to put these images in appropriate folders in Freesurfer. Thank you RB

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fast_selxavg3.m error/analysis.info file
by Yagmur Ozdemir 19 06 Feb '18

06 Feb '18

Hello FreeSurfer experts, I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output: #@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05 ------------------------- $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ ------------------------- outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log ------------------------------------------ rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1 The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated! Best, Idil

3 11

monte-carlo error in longitudinal pipeline
by miracle ozzoude 05 Feb '18

05 Feb '18

Hello Experts, I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page ( https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis) However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you. Best, Paul *Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd* GroupDescriptorFile 1 Class ADEX Input 1000_1 ADEX Input 1000_2 ADEX Input 1001_1 ADEX Input 1001_2 ADEX Input 1003_1 ADEX Input 1003_2 ADEX Input 1005_1 ADEX Input 1005_2 ADEX Input 1008_1 ADEX Input 1008_2 ADEX Input 1013_1 ADEX Input 1013_2 ADEX Input 1014_1 ADEX Input 1014_2 ADEX *Fsgd file 2: paired_diff.fsgd* GroupDescriptorFile 1 Class ADEX Variables Age Input 1000 ADEX 72 Input 1001 ADEX 76 Input 1003 ADEX 72 Input 1005 ADEX 80 Input 1008 ADEX 72 Input 1013 ADEX 80 Input 1014 ADEX 80

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FSFAST
by Ashley Cole 05 Feb '18

05 Feb '18

Hello, I have several nifti files. I have preprocessed some of them before. I used this command: preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm 5 -per-session -force The output files contained fmc.odd.sm5.self.lh.nii.gz, fmc.odd.sm5.self.rh.nii.gz, fmc.odd.sm5.mni305.2mm.nii.gz, and *fmc.odd.sm5.nii.gz*. Which this last one (fmc.odd.sm5.nii.gz) was the file that I needed for my further analyses. However, when I run the same command on another nifti file which was obtained from the same scanner and the same session, the output doesn't have the fmc.odd.sm5.nii.gz. I ran it several times but it never gave me that file. Also, it doesn't give me any errors. I appreciate any help. Ash

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Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file
by Chris Gorgolewski 04 Feb '18

04 Feb '18

Hi Dianne, You need to "mount" the using -v the same way input and output directories are mounted. For example: docker run -ti --rm -v /Volumes/Main/Working/BIDS_ TESTING/license.txt:/license.txt:ro -v /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer /bids_dataset /outputs participant --license_file /license.txt Best, Chris On Mon, Jan 22, 2018 at 7:13 PM, Dianne Patterson <dkp(a)email.arizona.edu> wrote: > Dear All, > > After trying the example bids app (which worked fine), I am trying the > freesurfer bids app. I have built the docker container on my mac and I have > the ds005 data directory here and the license.txt which I requested from > freesurfer. > I asked for a linux license (assuming the container contains linux and > that was the relevant fact). > > dpat@Saci:/Volumes/Main/Working/BIDS_TESTING% docker run -ti --rm -v > /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v > /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer > /bids_dataset /outputs participant --license_file "license.txt" > 1: You should define 'SliceTiming' for this file. If you don't provide > this information slice time correction will not be possible. (code: 13 - > SLICE_TIMING_NOT_DEFINED) > /sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz > /sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz > /sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz > /sub-02/func/sub-02_task-mixedgamblestask_run-01_bold.nii.gz > /sub-02/func/sub-02_task-mixedgamblestask_run-02_bold.nii.gz > /sub-02/func/sub-02_task-mixedgamblestask_run-03_bold.nii.gz > /sub-03/func/sub-03_task-mixedgamblestask_run-01_bold.nii.gz > /sub-03/func/sub-03_task-mixedgamblestask_run-02_bold.nii.gz > /sub-03/func/sub-03_task-mixedgamblestask_run-03_bold.nii.gz > /sub-04/func/sub-04_task-mixedgamblestask_run-01_bold.nii.gz > ... and 38 more files having this issue (Use --verbose to see them all). > > Summary: Available Tasks: Available > Modalities: > 133 Files, 1.77GB mixed-gambles task T1w > 16 - Subjects inplaneT2 > 1 - Session bold > > > Traceback (most recent call last): > File "/run.py", line 165, in <module> > raise Exception("Provided license file does not exist") > *Exception: Provided license file does not exist* > =========== > If I provide the full path to the license file, it still fails: > > docker run -ti --rm -v /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro > -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer > /bids_dataset /outputs participant --license_file > "/Volumes/Main/Working/BIDS_TESTING/license.txt" > > Suggestions? How do I tell freesurfer where the license file is? > > Thanks so much, > > Dianne > > > > -- > Dianne Patterson, Ph.D. > Research Scientist > dkp(a)email.arizona.edu <dkp(a)u.arizona.edu> > or > diannepat(a)gmail.com > University of Arizona > Speech and Hearing Science 314 > 1131 E 2nd Street, Building #71 > <https://maps.google.com/?q=1131+E+2nd+Street,+Building+%2371&entry=gmail&so…> > (Just East of Harvill) > ============== > If you don't hear back from me (and you expected to), > I blame the University's new SPAM filter. > Please write to my gmail account. > ============== > Antipiphany: That moment when you realize how little you actually know > ============== > > -- > You received this message because you are subscribed to the Google Groups > "bids-discussion" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to bids-discussion+unsubscribe(a)googlegroups.com. > To post to this group, send email to bids-discussion(a)googlegroups.com. > To view this discussion on the web visit https://groups.google.com/d/ > msgid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6iV% > 3DDiZEcZfDkU8Nzjnn41pEiwcA%40mail.gmail.com > <https://groups.google.com/d/msgid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6i…> > . > For more options, visit https://groups.google.com/d/optout. >

2 6

Recon-all -nonuintensitycor
by Alexis Moscoso 03 Feb '18

03 Feb '18

Hello Freesurfer developers, I’m trying to run a recon-all on ADNI T1 images. Since these data have already been corrected with the N3 correction, I want to turn off N3 correction in the recon-all process so I added -nonuintensitycor after -all. However, when I run it, I get an error during the normalization step since it no nu.mgz file is generated and cannot be found by mri_normalize. I’d like to know how to do the everything except the N3 correction. 1) Freesurfer version: 6.0.0

2 3

aparcstat2table with new destrieux atlas
by Lisa Delalande 03 Feb '18

03 Feb '18

Dear FreeSurfer expert, I would like to use the new destrieux atlas for extracting anatomical data with the aparcstat2table command. Is that possible ? If yes can you give me the command ? Or give me some references that can help me ? Thanks in advance Best regards Lisa

3 2

# voxels above thresholds across aparc+aseg regions - mri_segstats?
by Makaretz, Sara Johanna 03 Feb '18

03 Feb '18

Hi FS group, My goal is to calculate the % of voxels in a given region that are higher than a region-specific threshold. This is what I've done so far for each subject: * recon T1 * coregister vol.nii to T1 * move aparc+aseg.mgz into functional space * mri_segstats --i vol.nii --seg aparc+aseg.functionalspace.nii --sum vol.aparc+aseg.stats to get NVoxels & mean stats For each subject, for each cortical region (Seg1001-1035 & Seg2001-2035), I now want to count the number of voxels that are above region-specific thresholds as found in thresh.lst, ie. ctx-lh-bankssts Seg1001 1.383697722 ctx-lh-caudalanteriorcingulate Seg1002 1.272858762 ctx-lh-caudalmiddlefrontal Seg1003 1.167540497 ... Do you have any advice on the best way to do this? I think I can use mri_segstats, but am not sure if I'm looking at the right arguments and/or if there is a more straightforward way to do this. This is what I have so far: foreach s (`cat s.lst`) / foreach seg (`cat thresh.lst | awk '{print $2}'`) set thresh = `cat thresh.lst | grep $seg | awk '{print $3}'` mri_segstats --i vol.nii --seg aparc+aseg.functionalspace.nii --id $seg --maskthresh $thresh --masksign pos --sum tmp.$seg.stats ...and then grep NVoxels from tmp.$seg.stats, grep total NVoxels from vol.aparc+aseg.stats, divide/echo into summary stats file? Thank you in advance for any advice! Best, Sara

2 1

Misalignment between functional and anatomical data with bbregister
by Rachel Bencic 03 Feb '18

03 Feb '18

Dear Freesurfer Team, I am an image processing novice and am trying to register resting-state data to an anatomical scan using bbregister. The T1s have been run through Freesurfer's reconall pipeline, and the EPIs have undergone the following preprocessing steps: - slice time correctoin - deobliquing - drop first few images - motion correction / volume registration - despike - temporal filter - smoothing (I tried registering EPIs that had been aligned to MNI space to the anatomicals, with similar outcomes.) Ultimately, I plan to use Freesurfer-generated ROIs (those from Yeo et al., 2011), based on the anatomical scan, to run graph theory analyses on the resting-state data. However, when I use bbregister, the files are grossly misaligned. Below is an image of the EPI file on top of the white matter surface (in green). You can see that the EPI file looks very large. Has anyone encountered this problem / does anyone have any suggestions as to what I might be doing wrong? Any help would be greatly appreciated. Thank you in advance for your time.

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Freesurfer January 2018