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30089 discussions

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. >

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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

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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

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# 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

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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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funcroi-table-sess: how to specify frames for multi-band data
by Keishi NOMURA 03 Feb '18

03 Feb '18

Hi all, I’m using : freesurfer-Darwin-lion-stable-pub-v5.3.0 I’d like to plot HRF for each condition for each subject, using data acquired by multi-band EPI. Here are the commands I used: funcroi-config -roi rh.V1.roicfg -label rh.V1.label -analysis RH_fwhm8 -force funcroi-sess -s ORI01 -roi rh.V1.roicfg -df sessdirfile # m: frames foreach m ( 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 ) funcroi-table-sess -s ORI01 -df sessdirfile -roi rh.V1.roicfg -analysis RH_fwhm8 -c ASonlineRH -map cespct -o ./ROI/V1/ASonlineRH/ORI01.f$m.txt -frame $m end Then I got an error like “Error: input frame = 2, input volume only has 1 frames”. I referred to the related questions: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15883.html https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017958.ht… It seems that there is nothing wrong with these commands, except for specifying the frames. One possibility is that using multi-band data is somehow causing trouble. I’m now using multi-band factor = 8 and TR = 0.8 sec, so then I set the frames to multiple number of TR = 0.8, and ran the commands again: foreach m ( 0.8 1.6 2.4 3.2 4.0 4.8 5.6 6.4 7.2 8.0 8.8 9.6 10.4 11.2 12.0 12.8 13.6 14.4 15.2 16 ) funcroi-table-sess -s ORI01 -df sessdirfile -roi rh.V1.roicfg -analysis RH_fwhm8 -c ASonlineRH -map cespct -o ./ROI/V1/ASonlineRH/ORI01.f$m.txt -frame $m end But still I get errors like “Error: input frame = 2, input volume only has 1 frames”. (when I used frame = 2.4. Hence, it seems that we cannot use non-integral inputs) So, my question is: (1) How should I specify frames when I use multi-band data? (2) Regarding (1), what temporal resolution do I get when I use TR = 0.8? (for example, TER = 0.8/20 = 0.04 or anything like that) (3) Or, is there anything wrong with my commands other than frames? Thank you, Keishi

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How to extract stats of the regions that is covered by large clusters
by Shatil, Anwar Shahadat 03 Feb '18

03 Feb '18

Hello Experts: After running mri_glmfit sim, I got below clusters: ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 16.567 56197 13752.71 -36.8 -15.5 55.0 0.00020 0.00000 0.00040 30900 180209.80 precentral 2 9.630 57862 3018.98 -29.7 -72.0 -10.1 0.00020 0.00000 0.00040 4620 23119.05 fusiform 3 9.488 162470 2465.82 -16.0 -79.3 7.4 0.00020 0.00000 0.00040 4108 19097.47 pericalcarine 4 8.845 35506 1860.62 -24.5 -79.0 23.1 0.00020 0.00000 0.00040 3375 15122.28 superiorparietal 5 6.223 84246 1019.33 -4.8 15.4 -6.3 0.00020 0.00000 0.00040 1760 6950.26 rostralanteriorcingulate However, Cluster-1 area is large compared to others and it actually postcentral, and some portion of paracentral region. How can I extract the stats for these regions? Thanks, Anwar ------------------------------------------------ Anwar S. Shatil Research Assistant, Medical Imaging Sunnybrook Health Sciences Centre Toronto, ON, M4N 3M5 Email: anwar.shatil(a)sunnybrook.ca<mailto:anwar.shatil@sunnybrook.ca> This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

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Spatial smoothing during preprocessing
by Ben Smith 03 Feb '18

03 Feb '18

Hi all, I read from the freesurfer discussion archives that when combining FSL FEAT with freesurfer, one should definitely NOT do spatial smoothing in the preprocessing when preparing to examine cortical data. https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11536.html However I can see that in the FSFast pipeline, 2D and 3D smoothing **is** included in the FSFast preprocessing. So: 1. I am guessing that the 2D smoothing applies only to the surface and is smoothing on the surface space. Is this correct? 2. I'm also guessing that the 3D smoothing applies only to the subcortical regions. Is all this also correct? 3. The freesurfer.feat.ppt guide does NOT contain any instructions for doing any smoothing on data derived from FSL. But I assume that, if smoothing is done during FSFast preprocessing but is not done when preprocessing in FSL, then smoothing will still need to be done at a subsequent point with the FSL data. But I don't see instructions on that in the Freesurfer FEAT documentation on freesurfer.feat.ppt. If I do FSL preprocessing+1st-level analysis with no spatial smoothing, and then proceed with the analysis, at which point do I apply preprocessing? Is there a guide specifically describing how to apply smoothing to data originating from FSL? Thank you very much to anyone willing to help! Best regards Ben _______________________ Ben Smith, MSc. Ph.D. Candidate University of Southern California https://bjsmith.github.io/ w | +1 213-740 7851 m | +1 323-385 9349 skype | ben.smith.nz

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Problems transforming T1 to talairach
by Helen Beaumont 03 Feb '18

03 Feb '18

I am using the command mri_convert -at transforms/talairach.xfm brain.mgz brain_in_tal.nii.gz to convert a native-space skull-stripped T1 image to talairach space. I used recon-all to generate the transform matrix, and the segmentation and everything look good. But the T1_in_talairach image is not good - the brains are ending up different sizes, and frequently have the posterior chopped off. Please what am I doing wrong? Should I be applying the inverse of the transform? Helen Beaumont PhD University of Manchester

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