Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

[Fwd: Re: Error with mri_vol2surf]
by Shantanu Ghosh 16 Jan '13

16 Jan '13

---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] Error with mri_vol2surf From: "Shantanu Ghosh" <shantanu(a)nmr.mgh.harvard.edu> Date: Wed, January 16, 2013 2:05 pm To: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> -------------------------------------------------------------------------- Hi Doug, problem solved. I used the command: mri_vol2surf --projfrac 0.5 --src ./volstat/AC066-rh-volume.mgh \ --out ./volstat/AC066.volumefile.mgh --hemi rh --regheader 002901 \ --float2int tkregister --fixtkreg --trgsubject fsaverage Thanks Shantanu On Wed, January 16, 2013 11:02 am, Douglas N Greve wrote: > Does /volstat/AC066-rh-volume.mgh exist? > what happens when you run > ls -l /volstat/AC066-rh-volume.mgh > > doug > > On 01/16/2013 11:00 AM, Shantanu Ghosh wrote: >> 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 >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging

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nu_correct problem
by zach.petr＠post.cz 16 Jan '13

16 Jan '13

Dear members, when I run recon_all -subjid name -autorecon1 process stops with ERROR at nu _correct. This happens for DICOM but also IMA file type. I tried several brains. Do you have any idea what is wrong? Thanks much, Petr Zach

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Freesurfer vertex wise area reference
by MAHINDA YOGARAJAH 16 Jan '13

16 Jan '13

Dear Experts, What references can I use in a write up for the use of area measures in both vertex wise GLM and ROI based analyses. I have looked at the recommended citation blurb on the website but see nothing about specific references for area. I am using FS v5.1 with the modified mris_ preproc to facilitate qdec/GLM area analysis. Thanks. Mahinda

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Cortical thickness analysis using *.nii files
by Sinead Kelly 16 Jan '13

16 Jan '13

Dear members, I am new to Freesurfer and to cortical thickness analysis so I would like to ask a very basic question that I cannot find the answer to online - is it possible to conduct cortical thickness analysis using T1 files in *.nii format? -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

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Speeding up mris_fix_topology
by "Falk Lüsebrink" 16 Jan '13

16 Jan '13

Hello all, I'm processing some high resolution data with an isotropic resolution of 0.5mm and I was wondering if it would be possible to speed up mris_fix_topology somehow. Due to the increased number of vertices and also increased number of defects this stage takes incredibly long (e.g. lots of days). It would be nice if the defects are handled separately of each other to parallize the process. Maybe by first estimating and specifying the number of defects. Then by being able to run multiple instances of mris_fix_topology for the same subjects correcting one or a range of defects each. Best, Falk

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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

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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

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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

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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

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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

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Freesurfer January 2013