Freesurfer February 2018

freesurfer@nmr.mgh.harvard.edu

119 participants
170 discussions

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

2 3

One Group (One Factor), Two Covariates
by stdp82＠virgilio.it 05 Feb '18

05 Feb '18

Hi list, in reference to One Group (One Factor), Two Covariates https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx that has been applied on FS-FAST fcMRI data I obtain three folder, respectively, for "main", "covariate 1", "covariate 2". What's meaning the sig.nii.gz that it is produced by mri_glmfit in each folder? Please correct my conclusions if they are wrong. 1 - In the "Main" folder, the sig.nii.gz contains the results of One-sample t test regressing out the effect of the two covariates. 2 - In the "Covariate 1" folder, the sig.nii.gz contains the significant cluster that are associated with the covariate 1 regressing out the effect for the covariate 2. 3 - In the "Covariate 2" folder, the sig.nii.gz contains the significant cluster that are associated with the covariate 2 regressing out the effect for the covariate 1. Thanks Stefano

3 5

Fwd: Re: One Group (One Factor), Two Covariates
by stdp82＠virgilio.it 05 Feb '18

05 Feb '18

2 1

How to compile FreeSurfer with CUDA?
by Markus.Mertens＠evkb.de 05 Feb '18

05 Feb '18

Hello Freesurfer experts, I am trying to compile FreeSurfer to make use of its CUDA capabilities. The precompiled version does not run on my system. But when I try to compile FreeSurfer I get the following error: # ./configure --with-pkgs-dir=/usr/local/centos6-x86_64-packages --enable-fermi-gpu ... configure: Getting OpenGL info... checking GL directory... gl directory is /usr/include checking windows.h usability... no checking windows.h presence... no checking for windows.h... no checking for OpenGL library... no configure: error: FATAL: GL not found, but needed for tcltkapps XawPlusapps kwwapps wxwapps. Use --with-gl-dir=... to specify But OpenGL is installed: # ll /usr/lib64/libGL.so* lrwxrwxrwx 1 root root 14 Jan 15 23:35 /usr/lib64/libGL.so -> libGL.so.1.2.0* lrwxrwxrwx 1 root root 14 Jan 15 23:35 /usr/lib64/libGL.so.1 -> libGL.so.1.2.0* -rwxr-xr-x 1 root root 452752 Jan 15 23:37 /usr/lib64/libGL.so.1.2.0* # ll /usr/include/GL/gl.h -rw-r--r-- 1 root root 80615 Jan 15 23:35 /usr/include/GL/gl.h # The configure script did not ask for CUDA, yet. But CUDA is also installed in /usr/lib64: # ll /usr/lib64/libcuda* -rw-r--r-- 1 root root 556000 Jan 13 2017 /usr/lib64/libcudadevrt.a lrwxrwxrwx 1 root root 16 Jan 13 2017 /usr/lib64/libcudart.so -> libcudart.so.8.0* lrwxrwxrwx 1 root root 19 Jan 13 2017 /usr/lib64/libcudart.so.8.0 -> libcudart.so.8.0.61* -rwxr-xr-x 1 root root 415432 Jan 13 2017 /usr/lib64/libcudart.so.8.0.61* -rw-r--r-- 1 root root 775162 Jan 13 2017 /usr/lib64/libcudart_static.a # Adding the option "--with-gl-dir=/usr/lib64" to the configure script does not help. What else could I try? Regards, Markus _______________________________________________________________ Evangelisches Klinikum Bethel gGmbH Akademisches Lehrkrankenhaus der Universität Münster Sitz der Gesellschaft Kantensiek 11 | 33617 Bielefeld Amtsgericht Bielefeld HRB 30169 Geschäftsführer Dr. Rainer Norden (Vorsitz) Dr. Matthias Ernst Dr. Maren Thäter Vorsitzender des Aufsichtsrates Pastor Ulrich Pohl

2 1

mpr2mni305 talaraich transformation error
by Dijkshoorn, A.B.C. (Aicha) 05 Feb '18

05 Feb '18

Hello free surfer developers, I am attempting to compute cortical thickness for anatomical ROIs in neonates, but for some of my subjects I get the following error when I run the auto-recon1 command: \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin leia.ds.umcutrecht.nl 14.5.0 Darwin Kernel Version 14.5.0: Sun Jun 4 21:40:08 PDT 2017; root:xnu-2782.70.3~1/RELEASE_X86_64 x86_64 recon-all -s N192_con_recon exited with ERRORS at Fri Feb 2 12:32:02 CET 2018 Is there any way I can work around this error? I've also attached the recon-all.log and the talaraich_avi.log in case it's of any use. Kind regards, Aicha Dijkshoorn

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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 February 2018