Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30098 discussions

spot checking results
by Krieger, Donald N. 07 Feb '16

07 Feb '16

Dear List, I have run recon-all -all on the same scan on two different machines likely running two different versions of Linux but in any case the runs were done with different numbers of cores. I haven't done anything fancy to compare that the results are identical except for some spot checks of individual files with md5sum. label/lh.BA4a.label shows up the same on both. mri/wmparc.mgz does not. Your comments would be welcome. Is there something about the non-ascii files, e.g. wmparc.mgz, which would make them show different checksums, e.g. inclusion of a processing time or some such? Do you have experience or suggestions for convincing ourselves that we are getting the same answers on different machines? ??? Thanks - Don

3 2

To use a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 07 Feb '16

07 Feb '16

Hi list, I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer.How can I do it?Should I use mri_label2vol? Thanks. Stefano

2 1

Paired analysis FSFAST
by Thục Trinh 07 Feb '16

07 Feb '16

Hello, I'm working on group analysis in fMRI activation using FSFAST. I tend to test whether any significant changed in fMRI activation within group across two time points ( pre-training vs post). I ran first level already. I still confuse about the concat data and the mri_glmfit command. Here are the command lines, I'm wondering if it runs exactly what I want it to do. -- idlist Input NCP140005_1 Input NCP140005_2 Input NCP140012_1 Input NCP140012_2 Input NCP140071_1 Input NCP140071_2 Input NCP140079_1 Input NCP140079_2 Input NCP140082_1 Input NCP140082_2 Input NCP140543_1 Input NCP140543_2 Input NCP140556_1 Input NCP140556_2 Input NCP140558_1 Input NCP140558_2 -- concat data isxconcat-sess -sf idlist -analysis work.sm5.lh -contrast con-v-arrow -o group2 -- FSGD file GroupDescriptorFile 1 Title Con-arrow Gr2 Class Defi Input NCP140005 Defi Input NCP140012 Defi Input NCP140071 Defi Input NCP140079 Defi Input NCP140082 Defi Input NCP140543 Defi Input NCP140556 Defi Input NCP140558 Defi -- run glm analyisis mri_glmfit --glmdir lh.paired.gr2-diff --y ces.nii --fsgd con-arrow_group2.fsgd --C mean.mat -- content in matrix contrast C = [ 1 0 ] Thank you, Trinh

2 1

Planum temporale measurement
by Adam David Felton 07 Feb '16

07 Feb '16

Hello, I checked the listserv history, but couldn't find an answer to my question: With the 2009 parcellation scheme, 1) does the planum temporale parcellation include the posterior ascending ramus (which Destrieux et al. 2010 seems to imply) and 2) does the planum temporale include the posterior descending ramus? Thank you! Adam

3 2

Freesurfer v6.0 + edit in v5.3.0 then rerun v6.0
by Tiril Pedersen Gurholt 06 Feb '16

06 Feb '16

Dear Freesurfer Experts, It is my understanding that Freesurfer v6.0 is at the verge of being released. Do you have a tentative v6.0 release data? Also, there is a beta version of Freesurfer v6.0. How stable is it? (Mostly thinking of the recon-all pipeline.) Some of our data has been processed in Freesurfer v5.3.0 (recon-all to structural T1 data) and then manually edited. Is there a downside to rerun this data processed in v5.3.0 (after manual edit) in v6.0? Or is it best (or advisable) to rerun this data from the original T1 data in v6.0 and then do a new round of manual edit? Best regards, Tiril ?? -- Tiril Gurholt Postdoctoral Fellow - Psychosis Research Centre University of Oslo, Norway

2 1

seq.info
by Ji Won Bang 05 Feb '16

05 Feb '16

Dear. Freesurfer team I used dcmunpack to convert DCM to nii. This command didn't generate seq.info (I couldn't find it). I'd like to create one by myself.... Do you know how I can check the scan parameters: sequencename nrows ncols nslcs rowpixelsize colpixelsize slcpixelsize ntrs TR I know that when I use: unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir /scan.info I can get sequencename, nrows, ncols... but then from where can I check the others? Thank you very much. Best, Ji Won

2 3

DTI - Tracula question
by Alan Francis 05 Feb '16

05 Feb '16

Hi Anastasia: I am working on a set of DTI data that were obtained at the Martinos center. The data is in a single nii.gz file. The BVECS and BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file? Should I convert the nii.gz file into Analyze to get at the BVECS/ BVALS? thank you so much, best regards, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

3 7

Re: [Freesurfer] TRACULA Longitudinal can't find subject folder
by Deniz Gursel 05 Feb '16

05 Feb '16

Dear Anastasia, Thank you very much for your fast solution. Indeed, I was missing the related folders, I haven’t run the recon-all myself and I copied only the final folder and not the whole as a mistake. Now, I passed that error and got stuck with a new one. In the inter-subject registration step, I get the error: #@# Image corrections Fri Feb 5 14:34:25 CET 2016 mri_convert /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz mri_convert /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii... crypt_gkey = FS1gOHzYgoG2U TR=10443.18, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998789, 0.0474208, 0.0131247) j_ras = (0.0473438, 0.99886, -0.00611764) k_ras = (0.0133998, 0.00548885, 0.999895) writing to /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz... crypt_gkey = FS1gOHzYgoG2U if: Expression Syntax. #------------------------------------- /sw/freesurfer/5.3.0/bin/trac-preproc #------------------------------------- #@# Inter-subject registration (base template) Fri Feb 5 14:34:30 CET 2016 cp /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/mni2anatorig.mat /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/anatorig2mni.mat /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94/dmri/xfms cp: cannot stat ‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/mni2anatorig.mat’: No such file or directory cp: cannot stat ‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/anatorig2mni.mat’: No such file or directory Linux slow.mri.tu-muenchen.de 3.7.10-1.40-desktop #1 SMP PREEMPT Thu Jul 10 11:22:12 UTC 2014 (9b06319) x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Feb 5 14:34:30 CET 2016 I am attaching the trac_all.log, trac_all.error and dmrirc for you. Also, before the error, at the image correction step, there is “if: expression syntax” message which I couldn’t figure out why it happens. I looked it up and seems like some Unix error. I encountered it many times, when I was running another cross-sectional study and sometimes it went away magically. Thank you very much for your time and help.

2 1

use as seed a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 05 Feb '16

05 Feb '16

Hi list, I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer.How can I do it?Should I use mri_label2vol? Thanks. Stefano

1 0

tracula preproc complains about missing bvec-file
by Parzer, Peter 05 Feb '16

05 Feb '16

Hi, trying to do my first steps with tracula I got stuck early in the preprocessing step. The DICOM import and preparation for FSL seem to work (mri_convert, mri_probedicom, flip4fsl, fslswapdim, fslorient). But then trac-preproc wants to move a file named dwi_orig_flip.mghdti.bvecs that does not exist. What did I wrong? The command I used was trac-all -prep -c dmrirc The content of the configuration file "dmrirc" was the minimum as described in the tutorial: setenv SUBJECTS_DIR /dat/Hirnreifung/Auswertung/freesurfer set dtroot = /dat/Hirnreifung/Auswertung/freesurfer set subjlist = (3001LT) set dcmroot = /dat/Hirnreifung/Daten/DICOM set dcmlist = (3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm) dcminfo.dat and trac-all.log are in the attachments. Peter

3 4

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