Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30090 discussions

isxconcat ERROR:cannot find ERROR
by Emily Levin 19 Jul '13

19 Jul '13

Hello, I've been running into a problem when using isxconcat to run a group analysis. The command I've been using is: isxconcat-sess -analysis <name> -contrast <name> -sf sessidfile -o group.ffx.lh -df sesspar -hemi lh I am trying to concatenate data from 8 sessions, and whenever I run the isxconcat command I get this output/error: controls_meditators.group.ffx. lh/between_group.attendpassive.sm3.lh/log/isxconcat.log ERROR: cannot find ERROR:/bold_nopace/between_group.attendpassive.sm3.lh/dof I have a sessid file with all the sessions in it, and whenever I type sf -sessidfile it seems freesurfer cannot see which sessions to use, and instead looks for a file named error. When I run isxconcat with just one subject it works, but if I switch the subject isxconcat will continue to only run for the first subject I ran. I ran isxconcat on two groups (with 4 sessions each) and am now combining the groups to run all 8 sessions together. When I ran each group separately isxconcat worked just fine. The only difference now is that I symlinked the 8 sessions to a new project directory to run everything together. Any idea of what this error means and how I can fix it? Thank you, Emily

2 1

WM and pial surfaces problem
by LAOUCHEDI MAKHLOUF 19 Jul '13

19 Jul '13

Hi i run recon-all on a subject and when checking the surfaces, i noticed that a big part of the temporal part is badly segmented; this concerned WM as well as the grey matter. on the RecommendedReconstruction page, it is explained how to remove parts of non-pial structures considered as so, but not how to move the red surface to include missed wm and grey matter. thank you for help

3 3

Circular label of pre-defined radius on fsaverage
by sarahp＠nmr.mgh.harvard.edu 19 Jul '13

19 Jul '13

Hello FreeSurfer Experts, We would like to automatically create circular labels of a pre-defined radius (e.g. 14mm) on the fsaverage surface in freesurfer. For each label, a target vertex with pre-defined RAS/Talairach coordinates should be in the center. Would this be possible? Thank you, Sarah

2 1

Volumetric Analysis Inquiry
by Daniel LaFreniere 18 Jul '13

18 Jul '13

Dear FS Experts, I had a question concerning volumetric analysis. I will soon be starting this analysis and have exported my data into a text file using the flag: asegstats2table --subjects [list_of_subjects_for_analysis] --meas volume --tablefile asegstats.txt All of my subjects have the entire recon-all pipeline completed but nothing else. I'll be running my stats with SPSS but was wondering about intracranial volume (ICV aka eTIV). I read through the relevant info section on the FS wiki and it states that "correction [for the volume of the cranium] is performed because certain structures scale with head size...". However, I didn't see anywhere on the page stating if the correction for ICV (eTIV) is carried out automatically during the FS pipeline. Therefore, I'm wondering if ICV is accounted for when volumes are calculated within the aseg.stats file during autorecon3 (through mri_segstats and mri_label_volume). If not, do I have to do anything else to the data to ensure accurate analysis? I.e.: Should I account for ICV as a covariate during normal stats analysis or can I just run my analysis as I normally would and leave ICV out of the covariates? Thank you very much for your help, Dan

2 2

recon-all steps specified into volume and surface based stream?
by Martina Papmeyer 18 Jul '13

18 Jul '13

Dear FreeSurfer experts, I was wondering if there is anywhere a table or hint, suggesting which particular steps of all the recon-all steps (i.e. https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) are part of the volume-based or the surface-based stream or both? I also found this diagram https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllBlockDiagram but I'm unsure if the colours are supposed to give me any clues. I'm familiar with the broad processing stages of the two streams off course but would very much love to understand the details better :) Thank you very much for your help, Martina -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 1

Q) how to overlay two different maps in one template using different colors?
by Yune Lee 18 Jul '13

18 Jul '13

Hello Freesurfer experts, I'd hope to overlay two different results onto the same fsaverage template, but I'm not quite sure how to do it (I'm using free view). If anybody knows the trick, please give me help. thanks, ysl

2 1

pial surface midline fix
by Jason Tourville 18 Jul '13

18 Jul '13

Hi, I've encountered a recon-all'ed scan in which the pial surface along the posterior midline "jumps" on cortex in the opposite hemisphere. Is there a simple fix for this, perhaps using a hemisphere mask? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

3 2

freeview surface vertex point save?
by Jason Tourville 18 Jul '13

18 Jul '13

Hi there, The tksurfer/tkmedit combo allowed one to select and save a point on the inflated surface and then go to that point in the volume. Does freeview have a similar capability? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

3 2

Terminated Recon-all jobs
by Jonathan Holt 18 Jul '13

18 Jul '13

hey all, I've had a few jobs that were recently terminated due to a broken ssh pipe, is there anything i should do to before re-running those same jobs in order to avoid any issues? jon

4 3

mri_ca_normalize using -seg flag
by Mark Plantz 18 Jul '13

18 Jul '13

Hello freesurfers, I am currently trying to create a normalized .mgz file using the mri_ca_normalize command. Instead of using a .gca atlas, I am using a manually segmented image. I have tried using the -seg flag. However, I keep getting an error that I am not inputting the correct arguments. Do you have to include the .gca and transform file in the command, even if they will not be used? The fswiki section on GCA atlases does not seem to touch on this. For instance, which of the following would be the correct command line? 1.) mri_ca_normalize -seg <seg_file> <input volume> <output_file> or 2.) mri_ca_normalize -seg <seg_file> <input volume> <GCA atlas> <transform file> <output_file> Thanks for the help! ~ Mark

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