Freesurfer

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30093 discussions

mri_label2vol: Brodmann Areas
by Vincent Koppelmans 25 Feb '13

25 Feb '13

Hi all, I am trying to convert Brodmann area 4a and 4p to .nii file format in native space. I have used to following syntax: tkregister2 --mov ${SUBJECTS_DIR}/mri/rawavg.mgz --noedit --s [SUBJECT_ID] --regheader --reg ./register.dat mri_label2vol --label [PATH-TO-LABEL-FILE] --temp ${SUBJECTS_DIR}/mri/rawavg.mgz --subject [SUBJECT_ID] --hemi lh --o [OUTPUT-FILE-NAME] --proj frac 0 1 .1 --fillthresh .0 --reg [PATH-TO-register.dat-FILE] This is the result: https://dl.dropbox.com/u/6747155/BA4a.png As you can see, there are 'missing' voxels in the volume: it is not one smooth shape. However, when I convert aseg or aparc structures to volumes, I don't have this problem. Is it possible to get a a smooth, fully filled shape from a Brodmann label? Thanks in advance, Vincent

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Surface to native space
by Efrat Kliper 25 Feb '13

25 Feb '13

Dear freesurfer expert, We have preformed the full autorecon command using freesurfer and want to view the results in Slicer, When we load the pial surface onto slicer it doesn't seem to be coregister to the original MR image, how can we bring back the surface to the original native space or alternatively, how can we preforme the transformation on the original MRI so it will fit the surface that we gut. We found in the wiki a way to do that with volumes (mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz) but what about surface? We have also found the command mri_surf2surf, but not sure how to use it because we don't have surface in the native space? thank you in advance Efrat

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Merging .annot files using mris_label2annot puts labels in the wrong place
by Chris McNorgan 25 Feb '13

25 Feb '13

Hi all, I posted this back in January, and got a direct email reply from someone on the mailing list, who gave me a helpful tip, but it doesn't seem to be working out quite right. The problem: I have 3 .annot files per hemisphere, each based on the ?h.aparc.annot files (36 regions), but in each file, a different subset of these 36 regions has been further subdivided using the connectomemapper toolkit. I would like to merge all the subdivided regions, the definitions of which are spread across 3 files, into a single .annot file for each hemisphere. The one response I received said: After running cmtk on a subject you'll notice that in /FREESURFER/labels there are folders for each parcellation called "regenerated_?h_500" for example that contain all of the subdivided labels from that resolution Lausanne parcellation. I used mris_label2annot (http://surfer.nmr.mgh.harvard.edu/fswiki/mris_label2annot) to combine all of the desired labels into a single annot. The trick is that you need to type each label name one at a time with an --l flag (easy to make a script to do this quickly) and you need to supply a clut file, which has to be in the format freesurfer is expecting (which is also easy to generate, and the colors can be arbitrary). I've been trying this for a few days now without success. I also tried deconstructing the original .annot files using mri_annotation2label and then reassembling the label files using mris_label2annot (in the event that the label files I had been previously using were somehow mangled). Either approach seems to land me in the same place. The regions are generally in the right general anatomical area, but most are out of place within those regions. For example I've got renderings comparing the original definition of precentral_1 (highlighted region in purple in ORIGINAL.tiff), which has become precentral_20 (in REDONE.tiff). Similarly, parsoparcularis_10 has become parsoparcularis_1. But parahippocampal_1 was found in the paracentral region. All of these shifts look as though the label came from an adjacent region (alphabetically, as my ctab and scripts list the regions alphabetically). Also notable is that the left has 500 entries in the ctab file, but running my script gives the following output: ...<snip> 499 8697855 transversetemporal_3 500 8763647 transversetemporal_4 501 -1 NOT_FOUND Mapping unhit to unknown Found 1526 unhit vertices Similarly, the script for the right side also tries to map 503/502 entries. These errors and the fact that the reassignments look like they are off-by-one errors leads me to suspect that it might have something to do with my ctab files, as the region boundaries seem to be maintained. If anyone has any suggestions, I'm going to include links to the renderings, my scripts that execute mris_label2annot for each hemisphere, and my ctab files. I'm hoping I've left enough clues for someone to see where I'm going wrong. Thanks, Chris I've linked 7 files to this email: ORIGINAL.tiff <http://ubuntuone.com/1ABD5WZOw65wPj3NK2M69D>(1.0 MB)Ubuntu One <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/1ABD5WZOw65wPj3NK2M69D REDONE.tiff <http://ubuntuone.com/2PGqBjqUXCJl5RffOUkE3L>(1.0 MB)Ubuntu One <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/2PGqBjqUXCJl5RffOUkE3L lausanne_left.sh <http://ubuntuone.com/2PBnWtBTjXLCpVqxz7dgEP>(16.0 KB)Ubuntu One <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/2PBnWtBTjXLCpVqxz7dgEP lausanne_right.sh <http://ubuntuone.com/3uag3ZBIhRNisK2sB8MrhM>(16.1 KB)Ubuntu One <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/3uag3ZBIhRNisK2sB8MrhM lh.lausanne_annot.ctab.csv <http://ubuntuone.com/2PFJrAqBtLSxU3yqPpdpjU>(17.0 KB)Ubuntu One <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/2PFJrAqBtLSxU3yqPpdpjU rh.lausanne_annot.ctab.csv <http://ubuntuone.com/49H8V1gj7Ucq9FlIr8Onwg>(18.2 KB)Ubuntu One <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/49H8V1gj7Ucq9FlIr8Onwg lh.lausanne_annot.ctab.csv <http://ubuntuone.com/2PFJrAqBtLSxU3yqPpdpjU>(17.0 KB)Ubuntu One <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/2PFJrAqBtLSxU3yqPpdpjU Mozilla Thunderbird <http://www.getthunderbird.com> makes it easy to share large files over email.

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Registration & segmentation with FSL - obtaining correlation matrix..
by Sudhin A. Shah 25 Feb '13

25 Feb '13

Hello, This worked perfectly 2 years ago :), but now I am having some trouble. I run reg-feat2anat & aseg2feat with no problem. I now need a correlation matrix of every ROI (created by freesurfer) against every other ROI. For this I used @ROI_Corr_Mat (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) Again - this worked fine in the past. Now I get an error (working with AFNI to see if it can be fixed). Question: Is there any alternative to getting this correlation matrix? i.e every ROI against every other ROI? Thanks, S

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tkmedit error
by Ehsan Tadayon 25 Feb '13

25 Feb '13

Hello I'm new to freesurfer, I have some .nii images that i converted to .mgz via mri_converter in freesurfer and run recon-all on them! it seems everything is fine and i've got stats in m subjects folders. but when I try to do tkmedit to visualize images it gives me an error: Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. what should I do now?! thanks

2 1

mris_preproc --meas thickness
by stdp82＠virgilio.it 25 Feb '13

25 Feb '13

Dear fs users, I do not understand from tutorial if I should specify in mris_preproc --fsgd file.fsgd \--target fsaverage --hemi lh \ --meas thickness \ --target fsaverage --hemi lh \ --o lh.thickness.mgh the .thickness directory for each subject after --meas thickness. If yes, how can I do? Thanks, Stefano

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Re: [Freesurfer] \"nu_estimate_np_and_em\" error during recon-all
by Nick Schmansky 25 Feb '13

25 Feb '13

Thanks Anil! Tudor, sounds like you should give this a try. I'm re-posting this to the freesurfer list to archive it. Nick > > Hi > > I am having the same problem but I have an idea where it's occurring. > > I have Windows XP Virtualbox Ubuntu Install where I have an windows share > on the Linux using shared folder from windows > > When I use the shared folder it gives this error > When I use the Bert data set in its original location subjects dir it > works fine > When I transfer a new subject in virtualuser Freesurfer subjects folder > it's works fine > I ran it with -debug command to check and I thinks nu_ estimate makes some > temp folders which gets messed up when you use shared folders. > So to avoid this error transfer the subjects folder to virtualuser subject > folder rather than using -sd command to specify a shared folder > > Sincerely > > Anil > > > >

2 1

tkregister2 - stretching..
by Sudhin A. Shah 24 Feb '13

24 Feb '13

Hello, I manually checked the registration of my free surfer parcellations to the rsfMRI data after reg-feat2anat and aseg2feat. Problem is that I had to scale (stretch) the functional to make a good fit in several cases. Is this recommended? How can I avoid this? Thanks, S

2 3

5.2 ami
by Satrajit Ghosh 23 Feb '13

23 Feb '13

hi all, is there a public ami with freesurfer 5.2 available? cheers, satra

2 1

Pial boundaries
by melinaki p-t 22 Feb '13

22 Feb '13

Hello, I would like to ask if there are any commands or any manual edits I can use to fix the pial boundaries even if the white matter boundaries are fine. The white matter boundaries follow the white matter pretty good but there is some grey matter missing at some areas. Its not a massive problem though. Thank you in advance. Melina

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