Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

I receive an error when running recon-all with T1 and lesions from FLAIR
by Silas 26 Aug '16

26 Aug '16

Dear FreeSurfer team, I'm doing a structural analysis with 50 MS patients and 50 healthy controls (T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white matter. My co-worker did manual editing (bullet points) in the FLAIR images, and i would like to use these edits when running recon-all in order to avoid further manual editing. Steps in analysis: 1) First steps of recon-all: recon-all -autorecon1 -autorecon2 2) Reslicing the FLAIR images: The aseg.auto.mgz (256x256x256) didn't have the same size as the FLAIR (resliced to 1mm, co-registered in MNI-space and with manually drawn binary lesion masks (218x182x182)). I overcome this problem by reslicing the FLAIR images using aseg.auto.nii as the image defining space. This was done in SPM8, and prior to this the aseg.auto.mgz was converted to a .nii using mri_convert. 3) Insert lesions from the resliced FLAIR images to aseg.mgz: aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever format, but should be binary ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol ~= 0); newaseg = aseg; newaseg.vol(ind) = 77; MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so make a backup 4) The last steps of recon-all: recon- all -autorecon2-cp -autorecon3 When running the following command i get this error: /depot64/freesurfer/freesurfer.5.3.0/bin/recon-all -s 01MS -autorecon2-cp -autorecon3 subjid 01MS ............ '#@# Intensity Normalization2 Mon Aug DATE /.../subjects_FLAIR/01MS/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 5361 control points removed Building bias image mriMarkUnmarkedNeighbors: all inputs must be MRI_UCHAR or MRI_INT building Voronoi diagram... Numerical argument out of domain Linux big28 3.13.0-66-generic #108-Ubuntu SMP Wed Oct 7 15:20:27 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 01MS exited with ERRORS at Mon Aug 8 15:31:32 CEST 2016 The lesions looks alright (as if they are in the right place). Do you have any suggestions what to do if they are not? And what could be the problem if they are placed correctly? What is the advantage of starting by running autorecon-1 and 2 and then inserting the lesions from the FLAIR? Thanks a lot for all your help! Best, Silas

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Re: [Freesurfer] Recon-all error using Freesurfer 6.0
by Elpiniki Andrew 25 Aug '16

25 Aug '16

Thankyou! It worked when I removed the trailing " / ". However after it finished running, I received this error: ERROR reading /usr/local/DTI_processed_data/freesurfer_data_dir/fsaverage/label/lh.BA1_exvivo.label Because the "lh.BA1_exvivo.label" file for some reason, when I checked, was not in my subjects_dir. What should I do? Thankyou very much! Elpiniki Douglas N Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Mon, 22 Aug 2016 13:12:24 -0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Nothing looks suspicious. Try setting setenv SUBJECTS_DIR /usr/local/DTI_processed_data/freesurfer_data_dir ie, removing the trailing "/" On 08/22/2016 02:12 AM, Elpiniki Andrew wrote: > Hello Freesurfer experts, > > I'm having a bit of difficulty running the recon-all command. I > recently downloaded Freesurfer version 6.0. > > The command that I'm running is: > > recon-all -all -s $name -hippocampal-subfields-T1 > > However I keep receiving this error: > > If: Expression Syntax > > I've attached the output using the -debug flag. > > I'm using Linux ( centos6.3). Not sure if this is related but I > initially had an issue with recon-all stopped with an error when I > first ran the same dataset. There was an error in the log file " too > many levels of symbolic links". > So, I created a new subjects directory and created a symlink to the > fsaverage dir as per the instructions on the freesurfer wiki page. > > > Thankyou very much in advance for your time and efforts! > > Kind regards, > Elpiniki > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Understanding MNI305 alignment
by Christopher J Markiewicz 25 Aug '16

25 Aug '16

Hi all, This is the subcortical mask for a subject's functional data overlaid on top of $FREESURFER/average/mni305.cor.mgz: https://imgur.com/XQPwGVT The mask was produced with preproc-sess -s $SESS -fsd bold -nostc -per-session -fwhm 5 -mni305 Is the spread beyond the anatomical boundaries an artifact of the smoothing done, and thus we can simply apply ROI labels in MNI305 to the functional data, or does this suggest something has gone wrong in our preprocessing? Thanks, -- Christopher J Markiewicz Ph.D. Candidate, Quantitative Neuroscience Laboratory Boston University

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wmparc parcellation for thalamus and brainstem
by Dev vasu 25 Aug '16

25 Aug '16

Dear all, After running through recon-all ,I have obtained wmparc parcellation file (see the attached figure ). I would like to obtain parcellation at specific regions of interest for my study i.e Brain stem region and Thalamus region, could you please let me know how i could perform parcellation for these two specific regions of interest ( i.e. Brain stem and Thalamus ). Thanks Vasudev

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overlapping area question
by Arkadiy Maksimovskiy 25 Aug '16

25 Aug '16

Hello Freesurfers, I was wondering if someone might have information for how I can measure overlapping areas between a cluster that was generated as a results of a cortical thickness analysis, with a portion of a Yeo Network atlas. Specifically, I would like to calculate the percentage that the cortical thickness significant cluster (cache.th13.abs.sig.ocn.annot) overlaps with one region of the "lh.Yeo2011_7Networks_N1000.annot" overlay. I am not sure if there is a way to trace the two in tksurfer, and measure their overlapping area in that manner. Any help would be greatly appreciated. Thank you, Arkadiy

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Cannot allocate memory mri_glmfit to remove covariates
by Heidi Foo 25 Aug '16

25 Aug '16

Dear FreeSurfer team, I am currently running mri_glmfir --eres-save using FreeSurfer 6.0. However, there is an error saying "not enough memory to buffer." I have attached the error log for your reference. Do you have any idea how I can solve this problem? Thank you. Regards, Heidi

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GLM surface based cortical thickness analysis vs aparcstat table cortical thickness
by miracooloz＠gmail.com 24 Aug '16

24 Aug '16

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freeview error:
by Alison Boos 24 Aug '16

24 Aug '16

Hi FreeSurfer Team, I am trying to edit longitudinal data using FreeView. The original timepoints were processed and edited using FreeSurfer 5.1. The longitudinal data was also ran using FreeSurfer 5.1. I am currently trying to edit the longitudinal data using FreeView, however FreeView seems to have updated with the OS X and is incompatible with FreeSurfer 5.1. When I try to view the longitudinal base using FreeView errors pop up that say "failed to load". I don't want to update to FreeSurfer 5.3 for this project because it has all been run in 5.1 thus far. Does anyone have any insight about this? I'm using a MAC PRO (2009) with OS X 10.9.5 FreeSurfer Version: freesurfer-Darwin-leopard-i868-stable-pub-v5.1.0 FreeView Information: Process: freeview.bin [29818] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview.bin Identifier: freeview.bin Version: ??? OS Version: Mac OS X 10.9.5 (13F1911) Report Version: 11

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FW: Correcting for both hemispheres in thickness analysis using a PFC mask
by Gold, Andrea (NIH/NIMH) [F] 24 Aug '16

24 Aug '16

Hi, I have a question about correcting for 2 hemispheres in a thickness analysis using a PFC mask. Here are the steps I ran: 1) I ran the analysis in qdec without a mask. 2) I found the mri_glmfit.log file from step 1 and cut out the mri_glmfit command that runs the analysis and replaced ³label² option with path to our mask: cmdline mri_glmfit --y /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/y.mgh --fsgd /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/qdec.fsgd dods --glmdir /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151 --surf fsaverage lh --label /gpfs/gsfs3/users/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/lab el/labels/PFC_mask_8ROIs_LH --C /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/contrasts/lh-Avg-Intercept- thickness.mat --C /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/contrasts/lh-Diff-anxiousyo uth-healthyyouth-Intercept-thickness.mat 3) I then ran mri_glmfit-sim: mri_glmfit-sim --glmdir ./Thickness_LH_sm10_Dichtomous_n151 --sim mc-z 10000 1.3 mc-z.1p3.abs --sim-sign abs Question: I am 99% the mri_glmfit-sim command does not correct for both hemispheres. Is it possible to figure out if the cluster survives correction for 2 hemis based on the cluster summary file (attached) from steps 1-3 above?: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 2.480 124922 479.68 -7.2 29.0 -16.8 0.00440 0.00360 0.00530 887 medialorbitofrontal Thanks! Andrea -- Andrea Gold, Ph.D. Section on Development and Affective Neuroscience National Institute of Mental Health Room 201, Bldg. 15K, MSC 2670 Bethesda, MD 20892-2670 Phone: 301-827-9804 Fax: 301-402-2010 Email: andrea.gold(a)nih.gov <applewebdata://D38F487B-BA2B-4BF6-A9C4-96248AB2BE51/andrea.gold@nih.gov>

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PET surface sampling
by Jonathan DuBois 24 Aug '16

24 Aug '16

Hi, I’m trying to use the PETsurfer Pipeline to perform BP analysis, but I’m not sure at which point in the pipeline to sample the data to the surface and what registration to use? I tried running the pipeline using dynamic kinetic modeling as described here: http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer <http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer>, and then used the following command to try and sample the BP map the surface: mri_vol2surf --hemi lh --projfrac .5 --out_type mgh --cortex --mov mrtm2/bp.nii.gz --reg aux/bbpet2anat.lta --o lh.bp_pf5.mgh But got the following error: ERROR: source volume is neither source nor target of the registration I also tried sampling the mrtm2/bp.nii.gz to the orig.mgz volume space and then to the surface using: mri_vol2vol --mov mrtm2/bp.nii.gz --reg aux/bbpet2anat.lta --o mrtm2/bp_2anat.nii.gz --targ $SUBJECTS_DIR/subject1/mri/orig.mgz; mri_vol2surf --hemi lh --projfrac .5 --out_type mgh --cortex --mov mrtm2/bp_2anat.nii.gz --regheader subject1 --o lh.bp_pf5.mgh This worked, although the surface file did not have any values… Could you please let me know what is the best way to sample the data to the surface, and if it should be down prior to mri_glmfit or after. Thanks Jonathan

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