Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

report a bug
by salvatoreandrea.92＠libero.it 27 Nov '15

27 Nov '15

Hi! - I am using Ubuntu 14.4 (trusty). - This is my subject directory: /home/salvatore/freesurfer/subjects - This is the output of which recon-all (that is the tool I am trying to use): /home/salvatore/freesurfer/bin/recon-all - The command line that I run is recon-all -s /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis -i /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis/T1.nii.gz -all Following the error that I got after 12 hours of processing: sysname Linux hostname salvatore-HP-630-Notebook-PC machine x86_64 setenv SUBJECTS_DIR /home/salvatore/freesurfer/subjects cd /home/salvatore/freesurfer/subjects/FreeSurfer_analysis/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... Killed Linux salvatore-HP-630-Notebook-PC 3.19.0-33-generic #38~14.04.1-Ubuntu SMP Fri Nov 6 18:17:28 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s FreeSurfer_analysis exited with ERRORS at gio 26 nov 2015, 12.42.40, CET Could you please help me to fix this problem? I tried to ran it again in an other terminal, without succeding...Thank you Best, Salvatore

2 1

Quality Check of Subcortical Segmentation
by Jurij Wiede 27 Nov '15

27 Nov '15

2 1

mris_pmake bilateral
by Silvia Desiree Thielemann 27 Nov '15

27 Nov '15

Dear freesurfer experts, I want to calculate the distance between two vertices which are located on different hemispheres. I was wondering how I could do this with mris_pmake because a hemisphere is required within the analysis. Is there any possibility to obtain the distance between a vertices on the right hemisphere and a vertices on the left hemisphere? I already streamed out the maximum activated voxels which are my start and end vertices. Thanks in advance, Desiree

1 0

Multiple comparisons to confirm atrophy
by Clare Loane 26 Nov '15

26 Nov '15

Dear All, I have completed recon-all on my dataset of controls and patients. My patients have hippocampal/MTL atrophy and I would like to conduct multiple comparisons on the data to ensure that the atrophy is indeed focal in each patient and if not, identify where else atrophy is occurring in these patients. My hypothesis is that I do not expect atrophy elsewhere due to the disease type of these patients, but as this has never been confirmed outside of visual inspection before I wish to check this more robustly. I am not at all familiar with this kind of analysis and would like to ask some advice on how I should approach this? My initial instinct is to go with permutation testing. I would like to consider the whole brain (subcortical and surface). Are there other issues I should be taking into account? Any advice and specific information regarding the subsequent analysis in freesurfer would be greatly appreciated. Many thanks in advance. Clare

2 1

Error - extracting percent signal
by Danielle Miller 25 Nov '15

25 Nov '15

Hello freesurfer experts, I am trying to extract an average percent signal change from a functional roi label I created in tkmedit using fsaverage. I followed previously discussed methods: 1) mri_label2vol --label <name of label> --temp fsaverage/mri.2mm/orig.mgz --regheader fsaverage/mri/orig.mgz --o <name of label mask> 2) I checked (tkmedit fsaverage orig.mgz -overlay <label mask> -fminmax .5 1) and the label looked fine 3) I ran mri_segstats --i ces.nii.gz --seg <label mask from above> --id 1 --avgwf ces.label.dat ces.nii.gz is the file from my group analysis (isxconcat-sess) using the correct contrast It returns with this error: ERROR: dimension mismatch between input volume and seg input 163842 1 1 seg 76 76 93 Is there something I am doing wrong here? Also of note I tried using the following commands: 1) funcroi-config -label <label mask created from above mri_label2vol> -analysis <analysis directory> -roi <name of roicfg file> 2) funcroi-sess -sf sessid - roi <roicfg file from above> But this returns with this error: ERROR: cannot find /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_001_recon/label/label_lh_ACC_correct_mask.mgz Any suggestions would be extremely helpful. Thanks, Danielle -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130

2 1

voxel value scaling
by Rockers, Elijah D. 25 Nov '15

25 Nov '15

I am interested in finding a way to apply a slope scaling factor to the voxel values in a NIfTI image. I have done this in MATLAB and PMOD so far, but for some reason both methods change the origin or otherwise distort the dimensions of the image and render it impossible for me to process further. Something that simply scales the values without touching the header (or at least as little as possible) would be great. Is anything like this out there? Thanks, Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

2 2

Checking optseq efficiency of a custom par file.
by Sam Zorowitz 24 Nov '15

24 Nov '15

Dear Freesurfer list, Using the optseq2 program, is it possible to calculate the efficiency of a custom par file? I have an fMRI task that will be split into three blocks. I want to calculate the overall efficiency of my overall design byconcatenating the best par file from optimizing each individual block. I have already tried doing so by concatenating the three par files (updating the onset times) and inputting this into optseq2 by: >> optseq2 --in new_file.par --nosearch --tr 1.75 --ntp 1080 --psdwin 0 3.5 1.75 --o new_dir If I do this, however, I get a "core dump" error. Does anyone know how I might going about doing this? I've attached the new_par file for convenience. Best, sam

2 1

subjects_dir
by Eric Cunningham 24 Nov '15

24 Nov '15

Greetings Freesurfer experts, The README file in the $SUBJECTS_DIR says that a different directory can be specified by setting the env var SUBJECTS_DIR prior to the 'source $FREESURFER_HOME/FreeSurferEnv.csh' statement. Do the original contents of SUBJECTS_DIR (such as fsaverage) need to be moved into the newly specified SUBJECTS_DIR? Thanks, -Eric

2 3

Edit the number of segments in the segmentation of the corpus callosum
by UQAM 24 Nov '15

24 Nov '15

Hi, This a a "re-posting" of a question I've raised last week ; ) I would like to segment the corpus callosum into *twelve* even lenght segments instead of the five segments that freesurfer includes by default. - First I ran a mri_cc on subject e0070: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070 - Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see attachment, segments 251 to 262). - Finally I ran a mri_segstats to compute the statistics on segmented volumes. mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats The e0070_CC12.aseg.stats file still displays only five segments of the corpus callosum. Any tips or clues on how I could do things differently to get 12 segments? Thanks in advance, Geneviève

4 8

Cluster coordinates in QDEC
by henrike.hanssen＠web.de 24 Nov '15

24 Nov '15

1 0

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