Freesurfer December 2017

freesurfer@nmr.mgh.harvard.edu

107 participants
172 discussions

Building from source -- autoconf error
by Alle Meije Wink 29 Mar '18

29 Mar '18

I'm trying to build FreeSurfer from source on my Debian 8 (jessie) system. (64 bit, using g++ 4.9 for compilation) After $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev $ cd dev $ cvs update -d # just to make sure $ ./setup_configure I get these messages: rm -rf autom4te.cache libtoolize --force libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `config'. libtoolize: linking file `config/ltmain.sh' libtoolize: putting macros in `m4'. libtoolize: linking file `m4/libtool.m4' libtoolize: linking file `m4/ltoptions.m4' libtoolize: linking file `m4/ltsugar.m4' libtoolize: linking file `m4/ltversion.m4' libtoolize: linking file `m4/lt~obsolete.m4' libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree. aclocal aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: error: configure.in:2045: file 'm4/autotroll.m4' does not exist Which looks like a not-(anymore)supported use of autoconf? I found one previous message on the list about autotroll https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021854.… that provided another version of configure.in which might solve the issue. And it did in the original case but sadly not for me. I get the same error message also with the new configure.in -- there should probably be a configure.ac? If anyone knows how to make this work (e.g. by modifying the configure script) that would be fantastic.

8 17

mris_flatten error: bad vertex
by Ji Won Bang 20 Feb '18

20 Feb '18

Dear. Freesurfer experts. Hi. I'm having a problem with mris_flatten (version 5.3.0) Could you please help me fix this problem? My command line is: mris_flatten -w 0 -distances 12 7 $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat It returns the error: using write iterations = 0 sampling 7 neighbors out to a distance of 12 mm reading patch /home/jbang/Projects/replay/mri//replay06/surf/lh.oc.patch.3d with 30434 vertices (20.5% of total) MRISreadPatch: bad vertex # (148517) found in patch file No such file or directory When making the patch lh.oc.patch.3d, I followed the processes below: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast UpperLower select 3 points along a boundary between upper and lower visual fields (near calcarine sulcus) and press "Cut line". Then, select 4 points to define the cutting plane: 1 on lower side of the line, 2 on upper side of the line, 3 on the opposite surface (use rotation tool), and 4 to specify which portion of surface is kept, and press "Cur plane". File->Patch->Save Patch As lh.oc.patch.3d So I think I made the patch correctly. ! weird thing that I suspect is that when I click save patch as, the default location is $SUBJECTS_DIR/fsaverage/surf/ , so I had to change it to $SUBJECTS_DIR/$SUBJECT/surf Could you please help me? Thanks a lot! Best, Ji Won

3 4

Volume to Surface mapping looks great for Vols created in FSL but not SPM
by Rita Elena Loiotile 15 Feb '18

15 Feb '18

Hi, I'm trying to compare analyses that I've done entirely on the surface to analyses I've done in the volume. I'm comparing the analyses by projecting the volume analyses to the surface (HCP's 32k_fs_LR). The commands I'm using are: mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii; mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi}; It seems that the FSL volumes look identical to the surface analysis, when mapped. (Our surface analysis is mainly FSL-based, so this makes sense.) The SPM mapping, however, looks very odd. It isn't just that the intensity differs, but the localization of high intensity areas also varies. It seems that everything is shifted a bit superior and, possibly, posterior to the true location (as seen on the surface analysis). I'm wondering if I'm doing anything obviously wrong in my command usage. The brains were normalized to the MNI ICBM 152 template in SPM. I *think* it's suitable to use the -mni152reg flag in the command. I can attach pictures of the comparison if you'd like. Thanks in advance, Rita

3 5

[freesurfer] Extracting values of cortical thickness in each vertex.
by 박경일 09 Feb '18

09 Feb '18

Dear FS experts, I could get QDEC image comparing two groups. However, is there a way to get numerical values of cortical thickness in each vertex? Thank you Best, Kyung

3 10

Question about compare left and right hemi of longitudinal data
by lanbo Wang 24 Jan '18

24 Jan '18

Hi, all experts. I want to compare changes rate between left and right hemisphere of longitudinal data, How should I do that, how to combine xhemi with two stage or LME? Best, Lanbo

3 7

White/pial surface failure
by Trevor K Day 12 Jan '18

12 Jan '18

Hello, We are trying to run the high-resolution pipeline and it has failed spectacularly on one of our subjects. Two images from recon_checker are attached. I’m stumped because the command exits with an exit code of 0 and, in looking at the log, there no obvious indication of any error. I’m not sure what to search because I don’t have an error message. Recon-all.log is attached. The brainmask is fine. Not perfect, but certainly not poor enough to cause this. The intensity values of the T1 are perfectly normal, and there’s a bit of a motion artifact in the frontal lobe, but nothing that freesurfer hasn’t handled before. Others have suggested that this seems to extreme to fix with control points, are the other approaches to take? The command used was: /usr/local/freesurfer/stable6_0/bin/recon-all \ -all -s 170661.s1 -hires -cw256 -qcache \ -i /mnt/panuc/udallp2/subjects/170661/session1/mprage/T1_256.nii.gz \ -expert /mnt/panuc/udallp2/lib/expert.opts (Again, T1_256.nii.gz looks totally fine.) The contents of expert.opts are mris_inflate -n 30 * Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 * Platform: Debian GNU/Linux 8.9 (jessie) * Uname -a: Linux panuc 3.16.0-4-amd64 #1 SMP Debian 3.16.43-2+deb8u5 (2017-09-19) x86_64 GNU/Linux Where can I start to debug and fix this? Thanks, Trevor Day

2 7

Nonlinear CVS registration into average brain for coordinates
by Zhou, David Wei 10 Jan '18

10 Jan '18

Hi all, I have a data set of 14 subjects with intracranial (both cortical and subcortical) electrode implants, already recon'ed in Freesurfer, with an average brain + surface computed of these subjects. I would like to map each subject's electrode coordinates (a set of RAS points) into the average brain using a nonlinear transformation to account for individual deviations in surface topology. I'm trying to figure out the steps that must be taken to achieve this. With my average brain as a template, it seems like I would use mri_cvs_register to produce each subject warped onto the template. After generating those warps, how does one apply the same warp to a set of coordinates, for example to find out where my electrodes end up in the template brain? Which output file in .../cvs contains the data necessary to compute the coordinates in the template? I'd appreciate any instruction, thanks! David

3 2

Error using chol - FS-FAST selxavg3-sess
by stdp82＠virgilio.it 10 Jan '18

10 Jan '18

Running the "selxavg3-sess -s" command line in FS-FAST for seed-based functional connectivity analysis the following errors occurred: -------------------------- Temporally filtering Error using chol Matrix must be positive definite. Error in fast_selxavg3b (line 947) Wseg = inv(chol(toeplitz(acfrun))'); -------------------------- Thanks Stefano

2 7

How to output particular area from stats subdir
by Jing Gu 09 Jan '18

09 Jan '18

Dear FreeSurfer Developers, By using the following code, we can get volume data of different areas from stats file. asegstats2table --subjects N01 --meas volume --tablefile aseg_stats.txt How can I get information of one or two areas, such as hippocampal? thanks Best, Gina

2 1

Surfaces along midline
by Romella Durrani 09 Jan '18

09 Jan '18

Hi, I'm having problems with the surfaces along the midline for one scan. I have attached pictures of the brainmask with surfaces, wm.mgz, and T1 (before any of my edits). I have tried to fix this by adding control points and also tried to fix it by editing the wm.mgz file to fix the ventricle problem, however, none of these edits have resolved the issue. Thanks!

3 3

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Freesurfer December 2017