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freesurfer@nmr.mgh.harvard.edu

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30135 discussions

pial vs. aseg
by Wegbreit, Ezra 17 Oct '14

17 Oct '14

Dear Freesurfer community, 1. Does the cortical segmentation (tinted red in the attached aseg_vs_pial.png) need to follow the pial surface (red line) precisely? Does the region under the cursor that is marked as cortex but is outside the pial surface count in the aparc results? In general, should I fix pial surfaces so that aseg and pial match precisely? For this participant, the skull strip and white matter segmentation both looked really good, especially in this region. 2. What about small pieces of remaining dura (or other outside brain material) labeled red as cortex in the aseg? Do they count in cortical thickness values, even though there's a clear gap between them and the cortex proper? (see cortex_outside_brain.png) I did find this old post on the mailing list but I was unsure if it answers my question: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg03807.html >From what I gather from this post and some others*, the aparc results are based on the surface and the aseg values are only relevant to subcortical structures, but I am still unsure if this is the correct interpretation. The original question in the mailing list concerns the hippocampus, but my questions are about the top of the cortex. Many thanks for answers! Ezra * e.g., http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg07810.html *___________________________________________________________* *Ezra Wegbreit, PhD* NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Warren Alpert Medical School (401) 432-1615 ezra_wegbreit(a)brown.edu *___________________________________________________________*

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watershed error again
by Janosch Linkersdörfer 17 Oct '14

17 Oct '14

Hi all, I posted this problem earlier, but did not get an answer, so I am posting it again, sorry! --- recon-all runs smoothly for all my subjects but one. It throws the error "mri_watershed Error: indices out of bounds" and finishes (see https://www.dropbox.com/s/4del0uy8g1qw5az/recon-all.log ). The image quality does not seem to be different... The error has been discussed on the list ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021896.… ), but I don't know where in the brain and in which image space I should add control points or what else I can do to prevent this from happening. --- Thanks for your help, Janosch

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bbregister / mri_vol2vol with nifti file header
by Ajay Kurani 17 Oct '14

17 Oct '14

Dear Freesurfer users, I wanted to see if anyone knows what part of the file NIFIT header mri_vol2vol or mri_convert uses to write transform information from register.dat acquired from bbregister? I used the following commands to register the anatiomcal brain.mgz to the last time point of my EPI scan: bbregister --s ${sub}_FS --mov $bbrest_file --reg ${sub}_RS_register.dat --init-header --bold --frame $NP_last --nearest --template-out ${sub}.RS.template.nii mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ $SUBJECTS_DIR/${sub}_FS/mri/ brain.mgz --o $out_dir/brain_aligned.nii --inv --no-save-reg --reg $out_dir/${sub}_RS_register.dat When i view the images in Afni they look misaligned, but display perfectly in freesurfer (tkregister2 --mov EP_001.RS.template.nii --reg EP_001_RS_register.dat --surf) so I am assuming each program looks at a different field in the nifti file header. I used mri_vol2vol to apply the inverse transform of register.dat to brain.mgz so that it aligns with the EPI but for some reason it is not showing up correctly in afni so I wanted to get a better understanding of how freesurfer files write transformation information in nifti format (sform, qform, another part of the header) and if there is an easy way to get this into a format that afni reads correctly? Thanks, Ajay

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problem with gyrification index extraction
by elisa veronese 17 Oct '14

17 Oct '14

Dear FreeSurfers, I'm facing a problem with the estimation of local gyrification index. I've already performed the analysis with QDEC and the insertion of the MEASURE1 = pial_lgi line in the .Qdecrc file, but I'd like to see if it is possible to use the *aparcstats2table *command in order to have more concise and easy-to-read results. >From the QDEC GUI I've drawn a label in the temporal pole, and applied it to all my subjects (*mris_anatomical_stats -l rh.MR_TmpPole.label -t rh.pial_lgi -b -f s1/stats/rh.MR_TmpPole.stats s1 rh*) The problem is that when I call the *aparcstats2table --hemi rh --subjects s1 s2 ... --parc MR_TmpPole -t GI_MR_TmpPole.txt* I get a .txt file like this: rh.MR_TmpPole.area rh_rh.MR_TmpPole.label_area rh_WhiteSurfArea_area s1 6623.0 96171.8 s2 6257.0 85247.3 ... but I'm not sure what those numbers stand for. I'm afraid they have nothing to do with the gyrification index. Thank you, best elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php <http://icbn.uniud.it/tiki-index.php>*

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mkcontrast-sess errors no-octave
by elahe' yargholi 16 Oct '14

16 Oct '14

Dear Freesurfer experts, As I run mkcontrast-sess, I receive no octave error: fsl@fslvm6 MT_Localizer]$ mkcontrast-sess -analysis MT.lh -contrast MS -a 1 -c 2 INFO: Found 2 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 -1.00000000000000000000 mkcontrast -anadir MT.lh -wcond 1.00000000000000000000 -1.00000000000000000000 -sumconds -o MT.lh/MS.mat -wdelay 1 -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile MT.lh/MS.mat nconds 2, wcond 1.00000000000000000000 -1.00000000000000000000 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir MT.lh -wcond 1.00000000000000000000 -1.00000000000000000000 -sumconds -o MT.lh/MS.mat -wdelay 1 -no-octave Fri Oct 17 06:39:59 BST 2014 I have installed matlab and added path /home/fsl/Desktop/freesurfer/matlab /home/fsl/Desktop/freesurfer/fsfast/toolbox I will appreciate in advance if you possibly could help me to solve the problem. Best Regards, Elahe' Windows 7 and vmware10 Linux version: ------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/fsl/Desktop/freesurfer FSFAST_HOME /home/fsl/Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/fsl/Desktop/freesurfer/subjects MNI_DIR /home/fsl/Desktop/freesurfer/mni FSL_DIR /usr/local/fsl Current working directory: *pwd* */home/fsl* *which freesurfer* */home/fsl/Desktop/freesurfer/**bin/freesurfer* *which mkanalysis-sess* */home/fsl/Desktop/freesurfer/fsfast/bin/mkanalysis-sess* *which mkcontrast-sess* */home/fsl/Desktop/freesurfer/fsfast/bin/mkcontrast-sess* Command lines: *mkdir FIVA* *cd FIVA* *mkdir MT_Localizer* *cd MT_Localizer* *mkdir subj1sess1 * *cd subj1sess1* *unpacksdcmdir -src /home/fsl/Desktop/MTLocalizer/IMAGES -targ . -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii -run 11 bold nii f.nii* Within subj1sess1, made a text file named subjectname, and wrote subj001 (the name of my anatomical subject). *cd ..* *preproc-sess -s subj1sess1 -fsd bold -surface self lhrh -mni305 -fwhm 5 -per-run* For each run, a paradigm file (paradigm.par) is included. *mkanalysis-sess -a MT.lh -surface self lh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg* *mkanalysis-sess -a MT.rh -surface self rh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg * *mkcontrast-sess -analysis MT.lh -contrast M_S -a 2 -c 1 *

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FreeSurfer graphics requirement
by velocci＠physics.utexas.edu 16 Oct '14

16 Oct '14

Dear FreeSurfer users, I'm interested in using FreeSurfer on my Thinkpad X230 (Ivy Bridge) laptop with 8GB of RAM. My laptop does not have a dedicated graphics card, but rather an Intel HD Graphics 4000. Do you think I would still be able to run FreeSurfer, or should I really opt for a more capable machine? Thanks very much. I appreciate your time! Vince Velocci

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Freesurfer volume-based segmentation
by Gabor Perlaki 16 Oct '14

16 Oct '14

Dear all, I'd like to ask which steps are essential to check if I'm interested only in the volume based (aseg) results. I think Skull strip and Talairach transformation are essential. Any other steps I need to check? Thanks, Gabor

2 1

Convert "curv" into volume
by Roberta Santoro 16 Oct '14

16 Oct '14

Dear all, I am trying to convert the curv surface into a volume by using the following command: mri_surf2vol –surf curv –hemi lh –template $subj/mri/T1.mgz –surfval $subj/surf/lh.curv –projfrac 0 –volregidentity $subj –o CurvatureVolume.nii I get the following error: the lh.curv has many more faces than vertices! If the curv file is not a surface, is it possible at all to convert it into a volume? Thanks a lot for your help. Best, Roberta

3 7

Re: [Freesurfer] Centos 7
by will brown 16 Oct '14

16 Oct '14

Hi Zeke, I have completed a recon on CentOS 7. As far as I can see, the output matches the results from my previous recon of this subject using Freesurfer on CentOs 6. Is there any particular log that you would like to see? Will

2 1

Combining multiple transforms into one register.dat file for oblique angle acquisitions
by Ajay Kurani 16 Oct '14

16 Oct '14

Dear Freesurfer users, I had a question regarding how to combine multiple register.dat files into one file. Essentially, I have a T1 image which I created masks for in native space. I then import the T1 image into freesurfer and run through the recon-all pipeline. Subsequently, I use bbregister in order to register my last EPI timepoint to the T1 image and generate the register.dat file and when viewing the files the overlap looked great. 1) mri_convert -i m${sub}.T1.nii --in_type nii -o ${sub}.T1.FS.mgz --out_type mgz 2) bbregister --s ${sub}_FS --mov $bbrest_file --reg ${sub}_RS_register.dat --init-header --bold --frame $NP_last --nearest --template-out ${sub}.RS.template.nii 3) tkregister2 --mov EP_001.RS.template.nii --reg EP_001_RS_register.dat --surf I wanted to take my brain (freesurfer) and masks(native space pre-freesurfer) and the aseg file and then register this to the EPI scan and used the following commands: 4) Convert mask to freesurfer format mri_convert -i ${loc_dir}/spm/c1${sub}.T1.nii --in_type nii -o ${out_dir}/__c1${sub}.T1.mgz --out_type mgz 5) Take mask to brain freesurfer formatted space mri_vol2vol --mov ${out_dir}/__c1${sub}.T1.mgz --targ $SUBJECTS_DIR/${sub}_FS/mri/brainmask.mgz --regheader --o ${out_dir}/__c1${sub}.T1.FS.mgz --no-save-reg --nearest 6) Apply the inverse transforms of EPI to Anatomical so that the anatomical scans and masks are now registered with the EPI scan in native space (pre-freesurfer file). mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ $SUBJECTS_DIR/${sub}_FS/mri/brain.mgz --o $out_dir/__brain_FS2spm.nii --inv --no-save-reg --reg $out_dir/${sub}_RS_register.dat mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ $SUBJECTS_DIR/${sub}_FS/mri/aseg.mgz --o $out_dir/__aseg_FS2spm.nii --inv --reg $out_dir/${sub}_RS_register.dat --interp nearest mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ ${out_dir}/__c1${sub}.T1.FS.mgz --o $out_dir/__c1${sub}.T1.FS2spm.nii --inv --no-save-reg --reg $out_dir/${sub}_RS_register.dat --interp nearest The steps above work great when the T1, generated masks and EPI were all acquired plumb (no oblique angle). I tried using the steps for when the T1 (10.144 deg from plumb) and EPI (12.44 deg from plumb) were taken at 2 different oblique angles and the images did not register correctly when going back to native space. I essentially would not be able to apply the inverse register.dat directly to the aseg and mask files because when I did they did not look oriented correctly in afni (I did also try 3dWarp -deoblique on the resulting freesurfer files but this did not work for the oblique images). I wanted to see if I created two registration.dat files (One for EPI to Freesurfer's brain.mgz and another for the masks to Freesurfers brain.mgz) and combine these transforms into one file which I can pass to the native space images via commands in 6) so that they transforms are correct. OR am I wrong and there is a simpler way to achieve this. Please specify the commands to use in either case. Thanks, Ajay

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