Freesurfer

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30080 discussions

Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat
by Elijah Mak 26 Aug '16

26 Aug '16

Hi Anastasia, Yes indeed. I am using a dev version of freeview. I could give it another go with the freeview that came with v5.3. But does this mean that I shoudl also I re-run the tracula -stat on a v5.3? Thanks! Best Wishes, Elijah

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Visualising path.mean.txt in MNI space after trac-all -stat
by Elijah Mak 26 Aug '16

26 Aug '16

Hi Anastasia and others, I am trying to visualise the *.path.mean.txt on MNI template after running trac-all -stat. I used this command: freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w stats/*.path.mean.txt However, it looks like something has gone wrong with the labelling and position of the tracts (note the CST highlighted in green). https://www.dropbox.com/s/ndpkfgbrfgvt5q1/Screen%20Shot%202016-08-22%20at%2… Everything was fine and correctly labelled when I checked the merged tracks. Thanks again for your help! Best Wishes, Elijah P.S. On another note, the reinit=1 trick works very well and I was able to reconstruct the tracts in almost all cases. Thanks!

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Re: [Freesurfer] PET surface sampling
by Jonathan DuBois 26 Aug '16

26 Aug '16

Hi Doug, Thank you. I ran sampled the data and ran mri_glmfit as you suggested, although the resulting bp file seems to only have binary clusters (in the attached image the red cluster all have a value of 1 and everywhere else is 0). Is this the normal output? I expected a more varying map. Thanks Jonathan

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sig.sum files shows more clusters than sig.mgh image
by Oana Georgiana Rus 26 Aug '16

26 Aug '16

Dear Freesurfer experts, I have run an analysis on GM Volume in Freesurfer. The interested contrast was patients vs. controls. (/command mri_glimfit/) I then ran /mri_surfcluster/ command to get a text file with the significant clusters FDRcorrected and their peak coordinatesn- resulting in a *sig.mgh image* and a *sig.sum file*. *After looking at the sig.mgh image with tksurfer and searching for the significant clusters in the sig.sum files, I realized that one cluster which is pretty big is missing in the sig.mgh image but is present in the sig.sum file.* *Do you know why this could happen?Why is the image incomplete?* *Anybody encounterd something similar?* Because in the next step I want to extract the values of the significant clusters and correlate them with clinical scores, it would be good if thenumber of clusters in the result image and the result file coincide. Thanks in advance for your help. Best, Georgiana -- Oana Georgiana Rus PhD Student Neuroimaging Center TUM-NIC Klinikum rechts der Isar Technische Universität München Einsteinstr.1 81675 München Raum 5.8 Tel. 089 4140 7971

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modifying wm.mgz after editing aseg
by Julian Jäckle 26 Aug '16

26 Aug '16

Dear all my question would be whether editing wm.mgz and running autorecon2-wm will affect a previous edit of aseg? Further can aseg and wm.mgz be processed simultaneously as it is possible for wm.mgz and pial surface using autorecon2-wm? Greetings Julian

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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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