Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30091 discussions

Error with mri_vol2surf
by Shantanu Ghosh 16 Jan '13

16 Jan '13

Hi Freesurfers, Sorry if this is a newbie question. I receive the following error when I use mri_vol2surf to assign values from a subject volume file to each surface vertex and cant fix this ... mris_preproc command exits w/o errors in a previous step: mris_preproc --s AC066 --target fsaverage --hemi rh --meas volume --out volstat/AC066-rh-volume.mgh $ mri_vol2surf --projfrac 0.5 --src /volstat/AC066-rh-volume.mgh --out /volstat/AC066.volumefile.mgh --srcreg register.dat --hemi rh --float2int tkregister --fixtkreg srcvol = /volstat/AC066-rh-volume.mgh srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = tkregister GetProjMax = 0 INFO: float2int on the command line (2) overrides that in the registration file (0). INFO: float2int code = 2 mghRead(/volstat/AC066-rh-volume.mgh, -1): could not open file ERROR: could not read /volstat/AC066-rh-volume.mgh as type 3 Thanks for all the help. Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging

2 1

separate FSAverages and surface-based ROIs
by Paul Beach 16 Jan '13

16 Jan '13

Hello, I have two issues, currently. First, I was wondering if it would be possible to create separate FSAverage brains for different subject groups. I am working with healthy seniors and various stages of Alzheimer's disease, so doing so would be very helpful from the perspective of not conflating the differences in neuroanatomy between the these groups. One idea we had was to create separate HOME directories for each group, but we wanted to know if there was an easier way. I can't find anything in the interwebs about this. Second, I utilize some ROIs that are not specified by FS (such as secondary somatosensory cortex and anterior vs. posterior insula). My means of getting around this was to use FSAverage and tksurfer to hand-draw them, save them as '.label' files, map them to individual subjects, and export them to AFNI since much of our correlation analysis is done on that platform. However, I've noticed that when I view these hand-drawn ROIs in AFNI they only show up at the border of the gray and white matter, rather than filling the entirety of the gray matter. Note that this problem does not occur for ROIs in the look up table (like the caudal ACC). Exporting these to AFNI gives you a nice ROI that fills all the gray matter in the defined region. *Code I'm using*: For the latter problem, what I first use is mri_label2label to map the fsaverage-based ROI onto individual subjects, for example with the left anterior insula, before using mri_label2vol: *mri_label2label --srclabel lh.aIns.label --srcsubject fsaverage --trglabel lh.aIns.label --trgsubject [subj] --regmethod surface --hemi lh* *mri_label2vol --label ../label/lh.aIns.label --regheader aparc+aseg.mgz --o gmroi_volume.nii.gz --temp orig/001.mgz* Then I copy the new volume file to their AFNI folder, rename it, and run my correlation analysis on them. Note, that for those ROIs that are in the look up table (those parcellated by freesurfer) I simply use mri_label2vol before extracting them using 3dcalc (for example, the caudal anterior cingulate)... *mri_label2vol --seg aparc+aseg.mgz --regheader aparc+aseg.mgz --o gmroi_volume.nii.gz --temp orig/001.mgz* *3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,1002)' -prefix ROI_FS_lh.caudalACC.nii.gz* tl:dr Is it possible to "easily" create multiple FSAverages based on selected subjects (in my case, subject groups separated by disease state)? and Does anyone have any advice on how to get hand-drawn surface-based ROIs from Freesurfer's tksurfer into AFNI that full cover the entirety of the gray matter? Cheers and thanks! -- Paul Beach

2 1

mri_vol2surf sampling higher resolution
by Rouhollah Abdollahi 16 Jan '13

16 Jan '13

Dear Freesurfer, I have created a ribbon in high resolution like 0.5 x 0.5 x 0.5 mm^3 I selected some of those voxel in the high-res ribbon file. Then I wanted to create a paint file out of volume in that resolution on white or pial. I used the tkregister to register the high-res ribbon file to anatomy. then I used "mri_vol2surf --src seeg_in_ribbon.nii --src_type t1 --srcreg register3.dat --hemi rh --projfrac 1 --out ./seeg_in_ribbon_surface.w --out_type paint --surf pial" to project the volume on surface! but unfortunately I did not get any hits! I already know I should get some vertices but nothing is there!? INFO: output format is paint srcvol = seeg_in_ribbon.nii srctype = t1 srcreg = register3.dat srcregold = 0 srcwarp unspecified surf = pial hemi = rh ProjFrac = 1 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface /data/local/PROJECT/subj1/surf/rh.pial Done reading source surface Reading thickness /data/local/PROJECT/subj1/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 1 1 1 using old Done mapping volume to surface Number of source voxels hit = 122086 Warning: all vertex values are zero -- Best Regards Rouhollah Abdollahi

2 1

Problem autorecon2-cp with wm edits?
by Daniel Garcia 16 Jan '13

16 Jan '13

Hello all, I'm doing both wm edits and control points corrections to my image but it seems that the wm edits are not being taking into account when I'm using autorecon2-cp. At least the final wm.mgz image does not keep my previous modifications, but if I only run autorecon2-wm I can see that my modifications are preserved. Looking to the processing stages my only guess is that after the control points are applied there is a stage of Registration. If the registration changes even slightly due to the control points, won't be all the posterior images discarded (as the image moved?). I would like to try to unable the registration to see if I'm right but I don't really know if it will work or which stage I have exactly to skip. Doing first only control points and then only wm edits seems longer so I would like to do all the possible modifications at once. Thanks for your help Daniel

1 0

A question regarding volume calculation
by KimMJ 15 Jan '13

15 Jan '13

Dear experts I'm currently preparing a paper using the results of automatic volumetric segmentation of subcortical and cortical grey matter structures from aseg.stats and aparc.stats files.I have cited previous article by Desikan RS, et al (Neuroimage 2006;31:968-980) for the cortical GM volumetric segmentation, and Fischl B, et al (Neuron 2002;33:341-355) for the subcortical GM volumetric segmentation.At this point, my question is how volumes of these structures calculated. Is this volume of each GM structure based on surface area multiplied by cortical thickness? Apology for the newbie's question.Thank you in advance for your help. Kim MJ

2 1

peculiar postop recon?
by Borzello, Mia 15 Jan '13

15 Jan '13

Hey Freesurfers, Hope all is well in the new year! I ran a reconstruction with a postop MRI and for some reason it looks like part of the frontal lobe is getting cut off. Based on the patient's postop report, I would expect to see a temporal lobectomy. Thanks so much, Mia

2 1

error at ex-vivo entorhinal cortex label lh
by Terri Scott 15 Jan '13

15 Jan '13

Hello, I'm new to using freesurfer and I have gotten the following error when running recon-all on a new set of subjects. #@# Ex-vivo Entorhinal Cortex Label lh Tue Jan 15 09:25:23 EST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o KAN_adapt_02 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject KAN_adapt_02. processing subject lh.EC_average... MRIScomputeVertexSpacingStats: unsupported vertex set 0 eroding label 1 times before writing thresholding label stat at 0.400 before writing Linux mh21 2.6.38-16-generic #67-Ubuntu SMP Thu Sep 6 17:58:38 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s KAN_adapt_02 exited with ERRORS at Tue Jan 15 09:25:29 EST 2013 Everything seems to run fine up until this point. I need to run cvs on these subjects, will I need to re-run recon-all for cvs registration to work? Thanks, Terri

1 0

reversing recon-all resampling
by Jeff Eriksen 15 Jan '13

15 Jan '13

I have been asked to use FreeSurfer to create a good brain mask for use in another analysis stream (DTI and other things). I have chosen to do this by running recon-all on the structural scan, then taking the (aseg+aparc) and using FSL to dilate and erode to fill holes. This I binarize and rotate back into the same orientation as the original structural volume, and finally strip the padding added by recon-all, thus making the mask match the original T1 so it can be overlaid properly. The only problem is that, besides rotating and padding, recon-all also resamples to exactly 1.0 isovoxel, whereas the original T1 was 1.0 x 1.0 x 1.1 mm. Thus, I need to find a way to undo this resampling. Best I can determine this happens in the recon-all stream near the beginning where is seems to create some Talariach transform. Any ideas how to undo this xform, or can you suggest a better way to accomplish my goal. -Jeff Eriksen

3 4

Adding voxels
by Kristina Nalbandian 14 Jan '13

14 Jan '13

Hi can anyone give me some information on how I can add voxels. The gray matter that the arrow is pointing to was not included in the original recon-all -all and I was wondering if there was any way I could fix this problem during the editting. Thank you, Kristina Nalbandian

2 1

recon-all 5.2 not generating surfaces
by Jonathan Holt 14 Jan '13

14 Jan '13

In 5.0.0 I was used to dealing with brainmask.mgz files. in 5.2.0, I have so far been able to generate a T1.mgz, which to my eyes, looks OK. However, the resulting surf folder is empty and I'm not sure why. Log file attached. jon

3 2

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer