Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

(no subject)
by Jasmin Alves 19 Jan '16

19 Jan '16

Hello, I recently downloaded freesurfer on my mac with a Yosemite operating system. The application itself appears to work, however I am not able to use the command line to do any of the testing free surfer commands, as I keep getting a access denied. I have attached a screenshot. Your help would be very useful. Thank you, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

4 10

cortical and subcortical masks
by Nayyereh Ghazi 19 Jan '16

19 Jan '16

DearExperts,Iwant to create some cortical and subcortical masks to use as seed regions infsl’s Probtrackx and have faced some questions that ask you help me with them. Toextract subcortical regions I have used the below commands (e.g. for thalamus_r): {mri_label2vol \ --seg $SUBJECT_DIR/${subject}/mri/aparc+aseg.mgz \ --fillthresh 0 > /dev/null \ --identity \ --temp $SUBJECT_DIR/${subject}/mri/orig.mgz \ --o ${datadir}/aparc+aseg.nii.gz \ mri_binarize --i ${datadir}/aparc+aseg.nii.gz--match 49 --o ${datadir}/thalamus_r.nii.gz} I noticed that the number of voxels of the created masks inthis way are different from which is written in aseg.stats file. Could youplease explain the reason and the way to make these numbers as close as possible. For cortical regions I used both the above and below commands(e.g. for rh.superiortemporal):{mri_annotation2label --subject ${subject} \ --hemi rh \ --annotation$SUBJECTS_DIR/${subject}/label/rh.aparc.annot \ --outdir $SUBJECTS_DIR/${subject}/label\ --surface white mri_label2vol \ --label $SUBJECTS_DIR/${subject}/label/rh.superiortemporal.label\ --temp $SUBJECT_DIR/${subject}/mri/orig.mgz \ --identity \ --o ${datadir}/rh.superiortemporal.nii.gz\ --fillthresh 0> /dev/null}Again I have noticed differences in number of voxels of theresults from two methods for cortical regions and also a difference fromaparc.stats’s numbers. My final goal in to use the masks in probtrackx to findthe connections between subcortical structures and corticalregions in temporal lobe and I wonder which method is more accurate to create cortical masks. Also I want to know using which atlas is better for my purpose, aparc+aseg or aparc.a2009s+aseg. Your help is greatly appreciated. Wishes,Nayyereh

1 0

QDEC. Error in Analyze: command failed: mri_glmfit
by BAUTISTA-PERPINYA Maximilià 18 Jan '16

18 Jan '16

Hi there experts, I'm runing qdec to analyze my subject data. I am able to import the qdec.table.dat, but the problem comes in the Design step. I select 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 'LeftAmygdala' as the continuous variable. I don't select any nuisance factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but gives me the following error: --------------------------------------------------------------------------------------------------------------- ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 137 Checking inputs nframestot = 137 Allocing output Done allocing nframes = 137 Writing to /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh gdfReadHeader: reading /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 LeftAmygdala 1502.65 189.974 Class Means of each Continuous Variable 1 diagnosisBPD 1497.7548 2 diagnosisCCP 1540.8923 3 diagnosisNPC 1488.5490 INFO: gd2mtx_method is dods Reading source surface /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis --surf fsaverage lh --------------------------------------------------------------------------------------------------------------- Any recommendations? Any help is much appreciated :) Best, Max

3 3

error dwi2tensor
by Sanne Oostermeijer 18 Jan '16

18 Jan '16

Dear Freesurfer,experts, I am fairly new at DTI analysis. I have put together a script to pre-process my DTI data (attached). I have been able to succesfully run this for one of my datasets (T3) however, when I try to run the same script for my other set (T4), I get many errors popping up (see screenshot). The first part runs fine for T4; module 0 for mrconvert and 1 for eddy correction. As far as I know images from T4 are essentially the same from T3. I hope someone knows where the error comes from or can poijt me in the right direction. Thank you, Kind regards, Sanne

1 0

17 Jan '16

2 1

Hide small cluster in FDR corrected map
by stdp82＠virgilio.it 16 Jan '16

16 Jan '16

Hi list, I have performed a seed-based fcMRI analysis by FAST.After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurf.The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map.How is possible to do it?I have tried with mri_surfcluster.To have vwsig.nii.gz I should have a CSD file.But this file could be also produced when FDR correction is applied?I'm very confused.Please, could you help me because from several days I'm trying to have a solution.Thank you very much for your work.Kind regards. Stefano

1 0

Longitudinal analysis_covariates
by John Anderson 15 Jan '16

15 Jan '16

2 1

Cortical MS lesions - correcting pial surfaces
by Granberg, Erik Tobias 15 Jan '16

15 Jan '16

Dear FreeSurfer colleagues, We’re working with MS data and wanted your input on how we could best handle patients with extensive cortical pathology causing inaccurate reconstructions of the surfaces. In short the pial surfaces “dips” in too deep towards the WM surface due to the T1-hypointensity. A lot of the problems can be mediated by doing wm.mgz edits and actually including the lesioned tissues, which pushes out both surfaces to an accurate position. Sometimes though, the cortical lesion affects the whole depth of the surface and this trick does not help. Is there any way to directly push out or “anchor” the pial surface? Thank you for the help! Kind regards, Tobias Post-doctoral research fellow Multiple Sclerosis Imaging Group MGH/HMS/MIT Athinoula A. Martinos Center for Biomedical Imaging 149 13th St Charlestown, MA 02129

3 6

some questions about optseq
by charujing123 15 Jan '16

15 Jan '16

Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20 charujing123

4 19

15 Jan '16

Hi freesurfer list. I have a surface label for a region-of-interest in the right hemisphere, which I generated from a cortical thickness analysis. I am now doing an analysis on the white matter below this roi, by moving the label into volume space with mri_label2vol, and sampling below the surface with the --proj option. I want to repeat this white matter analysis in the homologous region-of-interest in the left hemisphere, as accurately as possible. I found the documentation for xhemi, and an earlier post about interhemispheric registration of rois ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-July/024821.html) but I'm not clear on what the xhemi option does, nor what the outputs are, nor what fsaverage_sym is, and so I haven't been able to figure out how to use it for my purpose. Is there more info available somewhere on interhemispheric registration with freesurfer tools, and/or does anyone have suggestions for how I should proceed? Thank you, Martha -- Martha M. Shiell, PhD

2 1

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