Freesurfer June 2011

freesurfer@nmr.mgh.harvard.edu

118 participants
168 discussions

WM edits with tkmedit make no difference
by Joel Bruss 03 Jun '11

03 Jun '11

I have a subject run through recon-all that has gross errors in GM/WM surfaces. I did my best to follow the ControlPoints tutorial on: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints My first try had >300 control points with no difference in the WM.mgz file. I stumbled upon the freesrufer.failure_modes.ppt and it states: "Don’t edit too much! This will reduce reliability and is almost never needed. Usually this means you need to start over as you’ve done something wrong (e.g. put control points in the wrong place)." I deleted my control points .dat file and tried again with only 12 control points, somewhat logically spaced throughout the whole brain. Still no improvement. Attached is a coronal image, typical of the error. So, what to do? Much of the normalized volume has values of 110 and it's my understanding that adding control points to values <110, that are known WM, will bring down the average value/tissue intensities. Here's a part of the stdout as I ran recon-all -autorecon2-cp -autorecon3 -subjid "subject": preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.1 +- 6.4 [80.0 --> 125.0] GM (74.0) : 72.4 +- 9.9 [30.0 --> 96.0] setting bottom of white matter range to 82.3 setting top of gray matter range to 92.2 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... My control points fall withing the WM range, as does much of the "110" labeled voxels, but the surface/WM.mgz file isn't improving. What am I doing wrong and what can I try next? Thank you in advance for any/all responses. -Joel

2 1

Problem in func2roi-sess
by John Richey 03 Jun '11

03 Jun '11

Dear freesurfer experts, I am having a problem in extracting ROI data using func2roi-sess, and any help would be most appreciated. I wish to evaluate functional data in two ROIs that I created using mri_cor2label (left and right amygdala). Here is the command line: func2roi-sess -roidef 54 -analysis autreg_analysis_vol -anatlabel 54 -s 20110519_12925 -maskthresh 1.3 Below, I pasted the relevant portion of the logfile produced by func2roi-sess. To the best of my understanding, at least part of the problem seems to be due to the fact that a file called COR-.info can't be found, nor can a file called "bold/001//../transforms/talairach.xfm". I've also tried it with the flag -labelspace tal (and native), but no luck. Should these have been produced by selxavg3-sess , or perhaps I am missing a step somewhere along the way? Many thanks, J Richey ... INFO: label2mask_linear: there were 2141 label hits voxsize = 60.8, rszthresh = 1e-07, thresh = 6.08e-06 INFO: label2mask_linear: there were 75 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 75 Done averging over ROI (nhits = 75) ------------------------------------------- /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925 mri_vol2roi --srcvol bold/001/ --roiavg bold/autreg_analysis_vol/54/-001 --srcreg bold/register.dat --label /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925/label/54.label --talxfm talairach.xfm --finalmskvol bold/autreg_analysis_vol/54/mask --roiavgtxt bold/autreg_analysis_vol/54/-001.txt ------------------------------------------- corRead(): can't open file bold/001/COR-.info -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925 mri_vol2roi --srcvol bold/001/ --roiavg bold/autreg_analysis_vol/54/-001 --srcreg bold/register.dat --label /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925/label/54.label --talxfm talairach.xfm --finalmskvol bold/autreg_analysis_vol/54/mask --roiavgtxt bold/autreg_analysis_vol/54/-001.txt version $Id: mri_vol2roi.c,v 1.32 2011/03/02 00:04:25 nicks Exp $ -------------------------------------------------------- roifile = bold/autreg_analysis_vol/54/-001 roitxtfile = bold/autreg_analysis_vol/54/-001.txt oldtxtstyle = 0 srcvol = bold/001/ srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925/label/54.label labelreg unspecified label fill thresh = 1e-07 mskvol unspecified Loading volume bold/001/ ...can't find talairach file 'bold/001//../transforms/talairach.xfm'

2 1

Differences between fsaverage and customized average surface
by soft.join Huang 03 Jun '11

03 Jun '11

Hi all: Now I have a customized average surface based on 50 subjects, using make_average_subject command. Loading the inflated surface in Freeview, I notice that there are some obvious differences between my template and fsaverage( not as smooth as fsaverage inflated surface, details in attachment ). I don't know whether it's reasonable or not. Is my customized template valid ? Thanks in advance. Best Regards, Lijie Huang

2 1

S_intraparietal-and_Parietal_transverse.label
by Esther Walton 03 Jun '11

03 Jun '11

Dear list, I am interested in the S_intraparietal-and_Parietal_transverse label from the Desitreux atlas using aparc.a2005s.annot. If I load this into fsaverage, it has three regions to it (see dark purple label in the attached screenshot): two big ones, very close to each other, connected by two narrow bridges, and another much smaller region more dorsally. Does this look fine to you?! Secondly, assuming this is ok, I created labels for each subject using mri_annotation2label and turned those labels into ROIs in standard space using mri_label2vol --label xx/label/lh.S_intraparietal-and_Parietal_transverse.label --temp xx/reg_standard/example_func.nii.gz --reg xx/reg/freesurfer/anat2std.register.dat --o xx/reg_standard/stats/lh.S_intraparietal-and_Parietal_transverse.nii.gz However, when I load this volume with: tksurfer fsaverage lh inflated -overlay lh.S_intraparietal-and_Parietal_transverse.nii.gz -mni152reg -fthresh 0.1 -fmax 1 it looks a bit off (see yellow label and red ROI in second screenshot). Would you think that's still ok taking into account the individual anatomy or did something go wrong somewhere? Thanks for your help, Esther

3 4

Unable to run mris_preproc and load data in qdec
by Jeanette Berberich 02 Jun '11

02 Jun '11

Hello! So, my first problem was that I wasn't able to load my new mgh files into qdec. I tried to follow this procedure: 1. Convert a curv file from you subject into mgh: mri_convert lh.curv lh.curv.mgh 2. Load in the mgh file to matlab lhcurv = MRIread('lh.curv.mgh'); 3. Replace the pixel data with your data: lhcurv.vol = myvector; 4. Write the result back out: MRIwrite(lhcurv,'lh.myvector.mgh'); 5. Do this for each subject 6. Run mris_preproc with --meas myvector --srcfmt mgh 7. Then run mri_glmfit http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03761.html My first question was that I wasn't sure if I needed to use preproc or not because all I want to do is replace my lhcurv.vol information and use that in qdec but I received the following errors: ninputs = 319 Checking inputs ERROR: dimension mismatch between /Volumes/Macintosh_Griffon_2/ParkHippoBrains/612/surf/lh.curv.fwhm5.fsaverage.mgh and /Volumes/Macintosh_Griffon_2/ParkHippoBrains/1165/surf/lh.curv.fwhm5.fsaverage.mgh Error in Analyze: command failed: mri_concat Followed by a list of all my files. So then I found this post: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-August/005918.ht… They had the same problem and the solution was that there had been too much separation between run recon-all qcache. I don't think this is my problem because I ran them all in 3 days, which I'm assuming isn't significant enough to cause such a problem. On that I'm wondering if I'm completely wrong and qcache is the problem. However, if that isn't the problem, I tried running mris_preproc and this is what happens [b417w74-196:/Volumes/KingRAID/ParkHippoBrains] kinglab% mris_preproc --target fsaverage --hemi lh --f list.txt --meas curv --srcfmt mgh --out lh.curv.fwhm5.fsaverage.mgh nsubjects = 321 tmpdir is ./tmp.mris_preproc.26297 /Volumes/KingRAID/ParkHippoBrains Thu Jun 2 16:44:03 MDT 2011 /Volumes/KingRAID/ParkHippoBrains --target fsaverage --hemi lh --f list.txt --meas curv --srcfmt mgh --out lh.curv.fwhm5.fsaverage.mgh Darwin b417w74-196.med.utah.edu 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 setenv SUBJECTS_DIR /Volumes/KingRAID/ParkHippoBrains tmpdir is ./tmp.mris_preproc.26297 \n\n --------------------------------------------------- #@# 1/321 155 Thu Jun 2 16:44:03 MDT 2011 -------------- ----------------------- mri_surf2surf --hemi lh --srcsubject 155 --surfreg sphere.reg --sval /Volumes/KingRAID/ParkHippoBrains/155/surf/lh.curv --sfmt mgh --trgsubject fsaverage --tval ./tmp.mris_preproc.26297/155.1.mgh --noreshape mghRead(/Volumes/KingRAID/ParkHippoBrains/155/surf/lh.curv, -1): could not open file. Filename extension must be .mgh, .mgh.gz or .mgz Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 155 srcval = /Volumes/KingRAID/ParkHippoBrains/155/surf/lh.curv srctype = mgh trgsubject = fsaverage trgval = ./tmp.mris_preproc.26297/155.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) Reading source surface reg /Volumes/KingRAID/ParkHippoBrains/155/surf/lh.sphere.reg Loading source data No such file or directory ERROR: could not read /Volumes/KingRAID/ParkHippoBrains/155/surf/lh.curv as type 3 I wasn't able to find any solution to this online and I'm not sure where to go from here! Thanks, Jeanette

1 0

recon-all very bad tlrc transform, how to fix?
by Jennifer Evans 02 Jun '11

02 Jun '11

Hey there, I have a very bad Talairach transform failure (from recon-all). The images from tmedit and tkregister2 are attached. The dataset itself is an unremarkable mprage, whose resolution etc. have worked for other subjects. The transformed output is rotated oddly leading to much stretching and badness. I played with aligning the transform in tkregister2 but it is too far out of alignment. How would I go about fixing this? (dataset was originally an AFNI brik and was converted to nii, if that gives clues as to the coordinate issue) Thanks, Jen

2 1

combining data from two sessions
by Finnegan Calabro 02 Jun '11

02 Jun '11

Hi all, we have a subject who had to end a run early, and as a result his data is split over two sessions. The two sessions can't be analyzed independently, since some events are missing from each, which causes selxavg3 to fail. Instead, what I've been trying to do is take the timecourses of the individual sessions and map them into a common space, and then re-run the functional analysis. Basically: - make_average_subject to get an averaged brain between the two runs - convert each fmcsm5.nii timecourse to this averaged brain - run selxavg3-sess on the combined data in the averaged brain space The averaged brain looks fine, but I'm running into problems on the second step. I've been trying to use mri_vol2vol for this, but I'm not entirely sure what to use for the target (if I use the T1 of the averaged brain, it'll be up-sampled into anatomical space, right? But I don't have anything else associated with the averaged brain to use). Does anyone know whether this is a reasonable approach for dealing with the situation? And if so, what should the mri_vol2vol command look like in step 2? This is still being done in freesurfer 4.5 for compatibility, but moving to 5.1 isn't out of the question if this has become easier to handle. Thanks! Finn

2 1

Error in generating V1 labels
by Shahin 02 Jun '11

02 Jun '11

Hi, I used the command: recon-all -s subjid -label-v1 to generate the V1 label for my individual subjects and I did not face any error. When I checked the label directory of the corresponding subjects, I see two new labels named lh.v1.predict.label rh.v1.predict.label but I don't see any ?h.V1.prob.label file (Actually I don't need them and I just need the thresholded ones). But when I load either of those files to tksurfer I don't see any label. Also, I can see this line on the command prompt: tksurfer.bin: no data in label file /good_subjects_anat/haas_anat/label/rh.v1.predict.label Would you tell me what is the possible error/problem? P.S.: I used both ver 4.5 and 5.0 and the result was the same. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

1 0

Error in recon-all on seychelles
by Chindhuri Selvadurai 02 Jun '11

02 Jun '11

Hello, I am not able to do a regular recon-all of my data on seychelles-- I am doing the same thing I used to do. We have started moving our data to a different location, however, since this is all new data, I don't see how this could be the problem. I am using freesurfer 4, so I set this var before sourcing the script: >setenv USE_STABLE_4_5_0 >source /usr/local/freesurfer/stable4 My subjects_dir is /space/ventzl/36/users/RespMon12C/subjects And my command is what it has always been: >/usr/bin/pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c 'recon-all -s RMOCD025 -all -i /cluster/archive/292/siemens/TrioTim-35006-20110504-155020-764000/764000-000004-000001.dcm -mail chinsel(a)nmr.mgh.harvard.edu -force' I would appreciate your help! Thank you, Chindhuri S ---------------------------- Original Message ---------------------------- Subject: PBS JOB 1380351.seychelles.nmr.mgh.harvard.edu From: "adm" <adm(a)nmr.mgh.harvard.edu> Date: Thu, June 2, 2011 2:03 pm To: chinsel(a)nmr.mgh.harvard.edu -------------------------------------------------------------------------- PBS Job Id: 1380351.seychelles.nmr.mgh.harvard.edu Job Name: pbsjob_14 Execution terminated Exit_status=1 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:01 Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

3 3

Error: talairach_avi: Command not found.
by ANN40＠pitt.edu 02 Jun '11

02 Jun '11

Hi all, I am running recon-all -autorecon1 -subjid subject and I have been getting an error saying: \n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n talairach_avi: Command not found. And then the program exits with errors. I looked in the transforms directory within my subject directory and there is not talairach.auto.xfm there. However, the other preceding output files are there. I am new to freesurfer and was wondering if anyone could help me figure out what I am doing wrong. Thanks, Ashley

1 0

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 June 2011