Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08
by Arsenije Subotic 06 Mar '19

06 Mar '19

External Email - Use Caution Hi, I am still struggling to examine differences in thickness using the command line stream for my two groups after controlling for age and sex. I get the following error when running the command line: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd CAA_CTRL_RH_Age_Sex.fsgd --C Contrasts/CAA-CTRL_Age_Sex.mtx --surf fsaverage rh --cortex --glmdir CAA_CTRL_RH_Age_Sex_Unix.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.000000 (col 5), Max=611.699463 (col 4) The scale is much different between columns 5 and 4, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 5, all values are 0 Column 6, all values are 0 Columns 5 and 6 are the same My design matrix is: 1 -1 0 0 0 0 (Examining difference in thickness after controlling for effects of age and sex) Iâ€™ve also attached the FSGD file that Iâ€™ve been using. Please let me know if there is something wrong with the file (although I have used a similar file without the covariates and did not have any issues). Thanks! Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1(a)ucalgary.ca<mailto:arsenije.subotic1@ucalgary.ca>

2 1

Masks in mri_segstats
by Zhi Li 06 Mar '19

06 Mar '19

External Email - Use Caution Hello Freesurfer experts, I would like to use mri_segstats with two different masks and thresholds, such as: mri_segstats --mask mask1 --maskthresh thresh1 --mask mask2 --maskthresh thresh2 This command can run smoothly with our any error. However, I am not clear if the results are correct. I mean if mri_segstats uses the overlap between two masks or only uses the last input mask and threshold? Any suggestions? Thank you and best regards, Lizhi

2 1

How to extract cortical features of a ROI
by 310913949 06 Mar '19

06 Mar '19

External Email - Use Caution Dear Freesurfer Experts, I want to extract cortical features of a ROI that I drawn manually on the rawavg.mgz in Freesurfer, but i don't know how to do that. I think maybe first the lesion mask should be registered to the standard templates fsaverage, but I don't know what the command line is , could you tell me? And secondly, I should use mri_label2label to map the label to individual subject and extract the cortical features of the ROI, am I right? I am looking forward to your reply!Thanks. Best wishes! Kan Deng

3 4

Resampling a gifti image to nifti using mri_surf2vol fails
by CAGNA Bastien 06 Mar '19

06 Mar '19

External Email - Use Caution Hi everyone, I need to convert a surfacic mask that is made from data of one subject projected onto fsaverage6 into a volumic map. To do so, I'm trying to use mri_surf2vol to take my Gifti file and create 3D version as Nifti file (using gray matter). So, I tryed this: mri_surf2vol --sd [subjects_dir] --subject fsaverage6 --o [output_filename].nii.gz --so [subjects_dir]/fsaverage6/surf/lh.white [lh.surf_mask_filename].gii --so [subjects_dir]/fsaverage6/surf/lh.white [rh.surf_mask_filename].gii But it failed and tells me: MRISreadGiftiAsMRI: no overlay data found in file [lh.surf_mask_filename].gii After quickly looking to the source code, at line 1077 of utils/gifti.cpp: /*----------------------------------------------------------- MRISreadGiftiAsMRI() - reads GIFTI functional frames into an MRI volume struct, which is a retro-fit usage to store multiple frames of data (where in this case, a frame is one complete vector of vertices). This routine will only read NIFTI_INTENT_TIME_SERIES data arrays. -----------------------------------------------------------*/ I'm getting confused because (from what I understood) this function is trying to read gifti's data in a nifti and moreover i didn't find any example on the web of resampling Gifti file to Nifti image using mri_surf2vol. I think I missing some think but do not understand what. Does any one have an idea about it? Best regards, Bastien CAGNA

2 1

Cerebellar Cortex Reconstruction
by Max Crayen 06 Mar '19

06 Mar '19

3 3

recon-all Workflow Help
by Riya Chatterjee 06 Mar '19

06 Mar '19

External Email - Use Caution Hi, I am new to FreeSurfer - I am a high school sophomore trying to learn more about processing brain MRI's. I have read through most of the documentation, but I was not sure about the workflow for processing an MRI. I am trying to extract just surfaces and was wondering if I can run "recon-all -autorecon2 -pial..." without running "recon-all -all...". Basically, I'm trying to see if I need to run the "recon-all -all..." step before running any of the sub-processes. I would greatly appreciate any advice I could get on this, thanks. Thanks, Riya C

2 1

Gradient Inhomogeneity Correction in Bay3
by Chinappen, Dhinakaran Maheswaran 06 Mar '19

06 Mar '19

Dear Freesurfer community, We acquired images in Bay3 and would like to know where the gradient inhomogeneity correction files would be on cluster, if any. We are familiar with the Bay4 procedure for correcting for inhomogeneity and were also wondering if similar steps would be followed for images acquired in Bay3. Thank you! Dhinakaran. -- Dhinakaran M. Chinappen Clinical Research Coordinator Neurology Department Massachusetts General Hospital m: 1-267-257-1224

1 0

mri_segstats issue with hippocampal subfields
by Daniel Callow 06 Mar '19

06 Mar '19

External Email - Use Caution Hello, I am trying to extract stats from the hippocampal subfield volumes that I have warped to diffusion space. mri_vol2vol --mov /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz --targ /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz --inv --interp nearest --o /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz --reg /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.dat --no-save-reg Then I run mri_segstats --seg /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --id 550 --id 552 --id 556 --id 557 --id 558 --i /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./fa-masked.nii.gz --sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.fa.stats using the --i id# from FreeSurferColorLUT.txt. However, looking at the values of the hippocampal subfield volume I see that the Id's are all in the 200's? Is there a txt file that has the labelings like in FreeSurferColorLUT.txt for these hippocampal subfields? Thank you for any help you can provide! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

3 4

extracting cortical parcellation
by Atena Rezaei 06 Mar '19

06 Mar '19

External Email - Use Caution Hello, I am trying to extract the cortical parcellation(atlas) file from freesurfer with all the labels. I found the lh.aparc.annot file in label folder. Should I use mri_annotation2label to create labels? or how can I extract the whole file? Thanks for ur help! BR, Atena

2 5

(no subject)
by Jahan, Bushra 06 Mar '19

06 Mar '19

Hello - I'm wondering how to generate a label in FreeSurfer from peak activation in a cluster? Is there a specific command?

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