Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

Qustion about Preprocessing for Tutorial_data
by 卯野賢太 03 Sep '09

03 Sep '09

Hi freesurfer gurus We are trying to preprocess of Tutorial fMRI Data. Following Freesurfer wiki,we adhered to hierarchy and type ' preproc-sess -s mgh-101.1 -fwhm 5'. But the following Error was displayed. ****************************** ************************************************************* [root@localhost my-study]# preproc-sess -s mgh-101.1 -fwhm 5 -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.log -------------------------------------------------------------- instem f mc 1 f fmc stc 0 fmc sm 1 fmc fmcsm5 mask 1 brain mgh-101.1 MC ----------------------------- 2009年 9月 3日木曜日 13:46:33 JST /usr/local/freesurfer/fsfast-tutorial/my-study mc-sess -fstem f -fmcstem fmc -s mgh-101.1 -d /usr/local/freesurfer/fsfast-tutorial/my-study -fsd bold -new -update -no-inorm ---------------------------------------- Logfile is /usr/local/freesurfer/fsfast-tutorial/my-study/log/mc-mgh-101.1-bold.log ------------------------------------------- /usr/local/freesurfer/fsfast-tutorial/my-study/mgh-101.1 RunList: 003 005 007 010 Targ Stem is 003/f ------- ************************** ----------- ------- Motion Correcting Run 003 ----------- ------- ************************** ----------- sess = mgh-101.1 2009年 9月 3日木曜日 13:46:34 JST mc-afni2 --i 003/f.nii --t 003/f.nii --frame 0 --o 003/fmc.nii --mcdat 003/fmc.mcdat /usr/local/freesurfer/fsfast-tutorial/my-study/mgh-101.1/bold mri_info --nframes --o /tmp/mriinfo.12296 003/f.nii log file is 003/fmc.nii.mclog mcdat file is 003/fmc.mcdat tmp dir is 003/tmp.mc-afni2.12296 #@# -------------------------------- /usr/local/freesurfer/fsfast-tutorial/my-study/mgh-101.1/bold mri_convert 003/f.nii 003/tmp.mc-afni2.12296/tempvol.nii.gz --nskip 0 --ndrop 84 -odt float mri_convert 003/f.nii 003/tmp.mc-afni2.12296/tempvol.nii.gz --nskip 0 --ndrop 84 -odt float nskip = 0 ndrop = 84 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 003/f.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9973, -0.0712038, 0.0179835) j_ras = (0.0625429, -0.951817, -0.300222) k_ras = (0.038494, -0.298286, 0.9537) changing data type from 4 to 3 (noscale = 0)... Dropping last 84 frames writing to 003/tmp.mc-afni2.12296/tempvol.nii.gz... #@# -------------------------------- /usr/local/freesurfer/fsfast-tutorial/my-study/mgh-101.1/bold mri_convert 003/f.nii 003/tmp.mc-afni2.12296/invol.nii.gz -odt float mri_convert 003/f.nii 003/tmp.mc-afni2.12296/invol.nii.gz -odt float $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 003/f.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9973, -0.0712038, 0.0179835) j_ras = (0.0625429, -0.951817, -0.300222) k_ras = (0.038494, -0.298286, 0.9537) changing data type from 4 to 3 (noscale = 0)... writing to 003/tmp.mc-afni2.12296/invol.nii.gz... #@# -------------------------------- /usr/local/freesurfer/fsfast-tutorial/my-study/mgh-101.1/bold 3dvolreg -verbose -dfile 003/fmc.mcdat -base 003/tmp.mc-afni2.12296/tempvol.nii.gz -prefix 003/tmp.mc-afni2.12296/outvol.nii.gz 003/tmp.mc-afni2.12296/invol.nii.gz 3dvolreg: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory ERROR: 3dvolreg ERROR: mc-sess failed ************************************************************************************************ If we need to download AFNI(or 3dvolreg),where should we put them(or 3dvolreg)? Please give us your suggestion. Thank you Kenta -- 卯野賢太 =================================== 早稲田大学スポーツ科学研究科修士課程１年卯野賢太早稲田大学フロンティアリサーチセンター所沢キャンパス 110号館〒359-1165 所沢市堀之内135-1 TEL：04-2947-6809 (内田研究室) unokentauno(a)gmail.com ===================================

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wiki page on how to read the stats files?
by Jared Price 02 Sep '09

02 Sep '09

Hi all, Does anyone know if there is a detailed wiki page on how to interpret each of the different stats files. To this point I have primarily used the aseg.stats file but one of the PIs we are working with wants a measure of total gray matter and total white matter specific to the frontal lobes. In the wmparc.stats file there are some values that are labeled ctx... and some labled wm... My initial understanding was that wmparc.stats contains only stats for white matter. Are these measures that start with ctx... actual measures of the cortex, or measures of the white matter underneath that cortex? If the ctx... ones are measures of the cortex, couldn't we just select the gyri that we wanted to include as part of the "frontal lobes" and then sum all the selected ctx... values (in order to get the measure for total frontal gray) and similarly sum all the selected wm... measures (to get the measure for frontal white) all from the wmparc.stats file?

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Wrong boundaries at ventricle.
by Hui Zheng 02 Sep '09

02 Sep '09

Hi freesurfer, We are reprocessing our data from FS version 3.05 with the latest 4.50. We found there are about 20% of the subjects have problem at the ventricle as shown in the attached image. I have tried the method suggested by Doug to remove the wm.mgz and rerun from autorecon2-cp. However, for two subjects I have tried, the method did not help. It will be tedious to manually fill in all the ventricles in wm.mgz. Any other work around? Thanks, Zheng Hui

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tksurfer failures
by Matt Sutterer 01 Sep '09

01 Sep '09

Hi all, I've tried running tksurfer to look at inflated hemispheres, and I can't seem to get my computer (or other machines for that matter) to show the entire inflated surface. All i get is a small bit of occipital cortex (that moves around and refreshes just fine), but I can't seem to get anything else to show up. I've been running freesurfer on sci linux 5 servers. Attached is a screen shot of what i get. Cheers, Matt

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FreeSurfer_volume_Talairach
by Judit Haasz 01 Sep '09

01 Sep '09

I assume my question has been skipped. sorry for bothering you again! Hi, I am trying to extract Talairach coordinates belonging to white matter volumes (wmparc subregions). Although tkmedit gives the coordinates for volumes, so far I have not found a feasible way by which I could print out the Talairach coordinates for each voxel index belonging to one region (volume) given by ColorLUT, eg lh-wm-parsorbitalis. Is there a way to do this? For surfaces I found out that each label file contains the list of vertices with RAS coordinates corresponding to one label. Ras coordinates can be converted to MNI, from which we can convert our region into talairach space by applying talairach.xfm. Is there a similiar approach that can be applied to volumes? I started by converting wmparc into Talairach space by mri_convert. Could you have a look at fornix segmentation? Thanks a lot, Judit Haasz

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Re: [Freesurfer] Problem with topology fixing
by Ed Gronenschild 01 Sep '09

01 Sep '09

Hi Bruce, The log file tells that mris_fix_topology did fail (euler number != 2) and that's why the topo_fixer was used. Ed On 1 Sep 2009, at 15:12, Bruce Fischl wrote: > did you try using the old (default) topology fixer? Usually > mris_fix_topology is called in recon-all unless you specify otherwise. > > cheers, > Bruce > On > Tue, 1 Sep 2009, Ed Gronenschild wrote: > >> Hi, >> >> I got the following error during processing my subject nr 104 with >> recon-all: >> >> ERROR: - FindPacePath: could not find path. >> >> The error log tells that it occurred during execution of the command >> >> mris_topo_fixer -mgz -warnings 104 rh >> >> What to do? >> >> Ed >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>

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Input/Output to specific atlas space/dimensions?
by Alexander Li Cohen 01 Sep '09

01 Sep '09

Hi all, Just starting using Freesurfer, and while I did search the mailing list archive, I didn't see a ready answer for this question: I would like to use Freesurfer to generate surfaces for my subjects (currently using Caret's SureFit routine), however I need to maintain a specific atlas space for my subjects (in this case, the WU 711-2B, T88-derived space). I can imagine two possibilities, but not how to do them, nor which is more accurate/appropriate: 1. Input the raw T1 for my subject in scanner space (1x1x1 isovolumetric) and then convert the Freesurfer surface and volume outputs to my atlas space using a previously defined linear affine transform (using local scripts written by Avi). This requires Freesurfer to back-convert all results to the original supplied space, then for me to additionally learn how to transform the surfaces. 2. Input the T1 for my subject already in my atlas space, and have Freesurfer output all results in the original supplied space. This, however, will be providing Freesurfer with data that has undergone an additional transform, but is obviously simpler.... in either case, the methodological question becomes simply: how can I tell recon-all to output all files in the original space provided. Given that it must perform the necessary transforms to get into the internal MNI305 space (I'm assuming), I'm simply wanting to undo all of the applied transforms. For obvious reasons, I want to use the same affine transform and transform routine consistently across this and my other datatypes. As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...) Many Thanks! -Alex Li Cohen ~)----------------- ---------------------------------------------------------------------- Alexander Li Cohen alexc(a)npg.wustl.edu (WORK Email) alexcohen(a)gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine ---------------------------------------------------------------------- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Problem with topology fixing
by Ed Gronenschild 01 Sep '09

01 Sep '09

Hi, I got the following error during processing my subject nr 104 with recon-all: ERROR: - FindPacePath: could not find path. The error log tells that it occurred during execution of the command mris_topo_fixer -mgz -warnings 104 rh What to do? Ed

2 1

isxconcat-sess error
by Garth Coombs 31 Aug '09

31 Aug '09

Hi, I've been running into a problem when trying to run a group analysis. When I go to run isxconcat-sess, I use this command: isxconcat-sess -sf hc.txt -df sesspar -analysis Ext -c CS+lvsCS-l - percent -o ./HC-Ext-083109 -hemis -trgsubject fsaverage It runs through the whole isxconcat without stopping, and there appears to be the normal outputs. However, when I scroll through the text in the terminal window, the following error appears repeatedly (I think once for every subject, possibly for each hemi of each subject): Reading source surface registration /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/ ext005_anat/surf/lh.sphere.reg Done loading source registration surface Reading target registration /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/ fsaverage/surf/lh.sphere.reg ERROR: could not find volume /autofs/space/dinah_001/users/balaji/ SUBJECTS_DIR/subjects/fsaverage/surf/../mri/orig. Does it exist? Done loading target registration surface Mapping Surfaces (ext005_anat -> fsaverage) When I go to fsaverage's folder, the orig.mgz file does exist, but for some reason, it looks like it's trying to direct it into the surf folder and then back out and into the mri folder and having trouble for some reason. When I try to type in the cd command as it appears (with the /../), it does take me to the mri folder where orig.mgz is stored, so I'm not sure why I get the error. I run into trouble after I run mri_glmfit, when I go to run surf- sess. I get the error: grep: /autofs/space/ricki_001/users/brittany/ext_fmri/HC-Ext-083109/ session.info: No such file or directory ERROR: cannot find /autofs/space/ricki_001/users/brittany/ext_fmri/HC- Ext-083109/ext/register.dat and then it exits. So for some reason, it looks like, even though isxconcat and mri_glmfit run and give outputs, they aren't registering to fsaverage somewhere along the way and are therefore not giving all of the outputs I need. Any idea of what I need to do? Thanks! Garth

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Re: [Freesurfer] Longitudinal vs. Cross-sectional Volumes
by Elizabeth Selgrade 31 Aug '09

31 Aug '09

Hi Bruce, I'm using v.4.4. Is there any processing that I can do to remove the bias without having to rerun everything with the newest version? Thanks, Liz -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, August 31, 2009 2:17 PM To: Elizabeth Selgrade Cc: 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Longitudinal vs. Cross-sectional Volumes Hi Liz, what version are you using? Our newest longitudinal version removes this bias. cheers, Bruce On Mon, 31 Aug 2009, Elizabeth Selgrade wrote: > Hello FreeSurfer Users, > > I have been using the longitudinal stream to process four timepoints > for about 20 subjects. I've extracted 9 ROIs and gotten their volumes > for both the longitudinal segmentations and the cross-sectional > segmentations. I'm noticing that there are seemingly significant > differences in the volumes for the two processing streams. The > cross-sectional stream gives results that range from about 0.5% to 19% above the longitudinal volumes. > > Have any of you gotten similar results? > > I'm curious as to why this is happening. I'm using different tools to > register the volumes to two different spaces - tkregister2 & > mri_label2vol move my cross-sectional aseg.mgz's to native space. > Mri_convert moves the longitudinal aseg.mgz's to the base space. I > don't think the different spaces are the root of the problem, as they should have the same resolution. > Could the different tools be affecting the size of my ROIs? > > Or, could initializing the longitudinal segmentation with the base > image somehow alter the volumes? > > Thank you! > Liz Selgrade > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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