Freesurfer

freesurfer@nmr.mgh.harvard.edu

22 participants
30073 discussions

mri_label2label dependencies
by Krieger, Donald N. 29 Aug '18

29 Aug '18

External Email - Use Caution Dear freesurfers, I am using mri_label2label with -regmethod volume . The only other switches I am using are minimal as you can see below. The thing is that none of the freesurfer stuff is in the srcsubject's directory. Why is there no error message? Where is it getting the stuff below the line: Src2TrgVolReg: ----------- ? Actually, I just need to know what to put into those directories so this function will work properly. I see from the documentation that I need mri/transforms/talairach.xfm in both the src and trg subject directories. Is there anything else that needs to be there? mri_label2label --trgsubject 174 --srcsubject subNo1 --trglabel /dev/shm/32089_labels --srclabel /dev/shm/32089_tmp0-2 --regmethod volume srclabel = /dev/shm/32089_tmp0-2 srcsubject = subNo1 trgsubject = 174 trglabel = /dev/shm/32089_labels regmethod = volume usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/pkg/freesurfer//subjects FREESURFER_HOME /usr/local/pkg/freesurfer/ Loading source label. Found 33 points in source label. Starting volumetric mapping 33 points Src2TrgVolReg: ----------------- 0.963 -0.002 -0.044 0.330; 0.034 0.930 -0.328 -0.544; 0.044 0.285 0.919 13.268; 0.000 0.000 0.000 1.000; 0 55.0000 17.0000 23.0000 52.2444 9.6043 41.6544 1 47.0000 1.0000 39.0000 43.8696 -10.7903 51.4429 2 52.0000 -4.0000 28.0000 49.1826 -11.6594 40.1300 3 55.0000 17.0000 16.0000 52.5536 11.8998 35.2230 4 50.0000 -10.0000 23.0000 47.4912 -15.6659 33.7380 Writing label file /dev/shm/32089_labels 33 mri_label2label: Done Thanks - Don

2 2

Designing Constrats for 3 Group 1 Covariate Analysis
by O'Dell, Ryan 29 Aug '18

29 Aug '18

External Email - Use Caution Dear freesurfers, I have what is likely a basic question but I'm new not only to FreeSurfer but contrast matrix design and group analysis as well, and was hoping for some help/clarification. Basically I want to run a GLM on our structural/functional data in order to determine if there's any significant correlation between cortical thickness and cortical amyloid deposition (measured by PiB), factoring in any potential effects of APOE genotype (e3e3, e3e4, e4e4). This means I want to construct an FSGD file with a 3 groups (the 3 APOE genotypes) and 1 covariate (our calculated cortical composite PiB value) for this analysis. However, I'm struggling with the proper contrast designs which test the various hypotheses in such a setup. Any answers, thoughts, or insights would be greatly appreciated. I know this type of analysis is also likely QDEC-able, but I think the FSGD approach would be more beneficial for my understanding of contrast matrix design. Please let me know if I've left out any information that could potentially help clarify my question/request. Best, Ryan O'Dell MD/PhD PGY2 Psychiatry Resident, NRTP Yale University

2 1

Convert mgh to gii
by David.Mackarthy 29 Aug '18

29 Aug '18

External Email - Use Caution Hi FS experts, I ran surface based analysis between two groups. The final output "is cache.th13.pos.sig.cluster.mgh" I would like to convert this file to gii format using "mris_convert" I tried: mris_convert -c cache.th13.pos.sig.cluster.mgh cache.th13.pos.sig.cluster.gii Please what I am doing wrong? Thanks for help -Dev

2 1

mri_gtmpvc for partial volume
by miracle ozzoude 29 Aug '18

29 Aug '18

External Email - Use Caution Hello, Can i specify a lookup table when using mri_gtmpvc? This is because I have a non-freesurfer segmentation (MALPEM) and i would like to perform partial volume on it without having to run freesurfer on the subject for PET analysis. I have a lookup table for the segmentation. I know mri_gtmpvc expects (?.ctab) file from the segmentation however, it will require processing the subject with freesurfer and petsurfer. I only want to use the partial volume command. How do I make it use the lookup table i made rather than ?.ctab file? Thank you. Best, Paul

2 1

input to mris_preproc
by Alon Baram 29 Aug '18

29 Aug '18

External Email - Use Caution Hello, I have a surface measure calculated for each of my subjects, which I have already resampled and smoothed on fsaverage using mri_surf2surf, i.e for each subject I run: mri_surf2surf --hemi <hemisphere> --s fsaverage --sval <surfMeasureSubjX> --fwhm <FWHM> --cortex --tval <output> I now want to stack the outputs of the commands above, so that I can give the stacked image as an input to PALM. I think I should use mris_preproc for that, but I'm not sure if the subjects (the argument after the --s flags) should be the original subjects or fsaverage - given that my surface measures are already resampled to fsaverage. That is, I'm not sure if the correct command is (for 2 subjects) mris_preproc --out <outfile> --target fsaverage --hemi <hemisphere> *--s subj1 --s subj2* --is <surfaceMeasureFileSubj1> --is <surfaceMeasureFileSubj2> *or * mris_preproc --out <outfile> --target fsaverage --hemi <hemisphere> *--s fsaverage --s fsaverage* --is <surfaceMeasureFileSubj1> --is <surfaceMeasureFileSubj2> Thanks!

2 1

smoothing only on cortex when using mris_preproc
by Alon Baram 29 Aug '18

29 Aug '18

External Email - Use Caution Hello, When smoothing with mri_surf2surf, it's possible to use the --cortex flag to constrain the smoothing only to cortex (exclude the medial wall and zero it out). Is there a way to tell mris_preproc to do the same (i.e to pass the --cortex flag when it calls mri_surf2surf? thanks!

2 1

create surface mesh from arbitrary volume?
by Russell Butler 29 Aug '18

29 Aug '18

External Email - Use Caution hello, i would like to create a mesh, such as the one in surf/lh.pial, using an arbitrary binary volume. i'm aware that freesurfer can convert the subcortical volume ROIs to surfaces, does anyone know if this can be applied to an arbitrary binary volume? i would like to replicate the script by Anderson Winkler (see below) but instead of on subcortical aseg, on an arbitrary volume that i supply. is this possible? thanks, # Pre-tessellate echo "==> Pre-tessellating: ${s}, ${lab0}" ${FREESURFER_HOME}/bin/mri_pretess \ ${SUBJECTS_DIR}/${s}/mri/aseg.mgz ${lab} \ ${SUBJECTS_DIR}/${s}/mri/norm.mgz \ ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz # Tessellate echo "==> Tessellating: ${s}, ${lab0}" ${FREESURFER_HOME}/bin/mri_tessellate \ ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz \ ${lab} ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth # Smooth echo "==> Smoothing: ${s}, ${lab0}" ${FREESURFER_HOME}/bin/mris_smooth -nw \ ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth \ ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0} # Convert to ASCII echo "==> Converting to ASCII: ${s}, ${lab0}" ${FREESURFER_HOME}/bin/mris_convert \ ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0} \ ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc mv ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc \ ${SUBJECTS_DIR}/${s}/ascii/aseg_${lab0}.srf

2 1

LME Univariate pvalue inconsistent
by Wang, Xiaoyu 29 Aug '18

29 Aug '18

External Email - Use Caution Hello Freesurfer Developers, I'm attempting to use Univariate LME analysis to compare the symptomatic and asymptomatic hemispheres of early stage Parkinson's disease patients. I re-organized the data so that the symptomatic hemisphere is the left hemisphere and the Asymptomatic is the right (by flipping the orig.mgz before recon-all). I followed the LME model tutorial for univariate on the freesurfer wiki and created my qdec.tabel.dat to have the same layout as in the example with group 1 as left hemisphere and group 2 as right hemisphere. I have a design matrix to do a simple linear model containing a group by time interaction with the contrast of [0 0 0 1 0 0] After running the F-test however, I noticed that the p-value was really inconsistent across atlases. I used multiple atlases and noticed that the p-value can be as low as 1.00E-30 for many structures. This is too good to be true especially since after sending the thickness value to a statistician she came back with values greatly different from mine. However, the Bhat values were similar. Can someone give me a hint as to what is going on? Xiaoyu

2 1

fsaverage for a Left vs Right hemisphere Longitudinal Comparison
by Wang, Xiaoyu 29 Aug '18

29 Aug '18

External Email - Use Caution Hello Freesurfer Experts, I am trying to compare the left and right hemisphere of a group of PD patients with Mass-Univarate LME. >From what I can see in the wiki tutorial, the mris_preproc only assembles data from one hemisphere at a time, which is not very usefull if I am doing a hemisphere comparison where each hemisphere is a different group. I am thinking of getting around this issue by flipping each subject time point so that the right hemisphere is on the left and adding it as a new timepoint. For example: S01_1 s01_base S01_1f s01_base S01_2 s01_base S01_2f s01_base However, Can I still create the base file the same way using this? recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all also for the fsaverage, would make_average_subject still work? Xiaoyu

2 1

Manually editing location of surface
by Elena Nicole Dominguez 29 Aug '18

29 Aug '18

External Email - Use Caution Hello FreeSurfer Developers, On the tutorial it states that it is not possible to directly edit the location of a surface. However, on the corresponding video posted onto the website the gentleman mentions being able to accomplish this. I have been trying to locate the literature on how to do this and have not been successful. I am using 'freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c' I would kindly appreciate some help on locating any tutorials or information available. Thank you for your help.

3 5

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