Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

"rm:No match." when executing recon-all -qcache
by Yang, Daniel 15 Mar '13

15 Mar '13

Hi all, When I run "recon-all –qcache", there are a lot of Error messages saying "rm: No match." (although just this error message, no others). I'm wondering if this is something of concern, or something I can simply ignore. Thanks! Daniel

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subcortseg flag
by A. Yamamoto 15 Mar '13

15 Mar '13

Hi, After upgrading to FreeSurfer 5.2.0, the command with "-subcortseg" flag exited with the following error. MRISread(/usr/local/freesurfer/5.2.0/dist/subjects/test/surf/lh.white): could not open file The "-autorecon1" stage finished without error, so I'm wondering if there is any change in mri_segstats?? FYI, I have attached the last part of recon-all.log file. Thanks for your help. Akio

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mri_cvs_register - use of wmparc instead of aseg
by Güllmar, Daniel 14 Mar '13

14 Mar '13

Dear Lilla, i'm currently applying mri_cvs_register and I'm very happy with the nice results. Congratulation for this very clever approach. However, some data sets which I work on have still aseg.mgz which are not segmented appropriately. As far as I understand aseg.mgz is not redefined after e.g. pial-edits or added control points. Thus, I think it might be better to use aparc+aseg or wmparc instead of aseg within mri_cvs_register. Taking this into account I have the following questions: 1. Do you have experience with mri_cvs_register and --asegfname Option different from aseg? Does it impact the processing time? Are there options, which have to be adopted? 2. Since I think it is better to use aseg instead of wmparc, since it contains fewer IDs and registration will not be overfitted, is there a convenient way to generate a new aseg.mgz, which includes manual corrections like pial edits? 3. The last question regards the norm.mgz ... since it also often contains to much (outer brain) volume .. would it be better to mask norm.mgz with (e.g.) wmparc or a dilated version of wmparc before using it with mri_cvs_register ? Thanks you, Daniel Universitätsklinikum Jena - Bachstrasse 18 - D-07743 Jena Die gesetzlichen Pflichtangaben finden Sie unter http://www.uniklinikum-jena.de/Pflichtangaben.html

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Xhemi files do not exist in the specified ftp location
by Negar Memarian 14 Mar '13

14 Mar '13

Dear Doug, Can you please advise me of the correct location of the ftp directories/files required to be installed for surface based interhemispheric registration? I'm trying to download and install the required files from the specified path: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ but the files/folders (e.g., surfreg, mris_preproc , fsaverage_sym.tar.gz , etc) do not exist. I appreciate your help. Regards, Negar

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Process flow: ReconAllDevTable
by Mehul Sampat 14 Mar '13

14 Mar '13

Hi Folks, Based on the tutorials, we normally run full recon-all pipeline; then add control points if required and then run -autorecon2-cp and -autorecon3 again. Recently, I was looking at the process flow table: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable and I have two questions: 1. From this table it seems like ?h.white is created in autorecon2 and ?h.pial is created in autorecon3. However, when i run recon-all -s subj -autorecon1 -autorecon2 i see that ?h.pial is also already created. Does this mean I am interpreting the process flow table incorrectly or is there an error in the table ? 2. Also if ?h.pial and ?h.white are already created at the end of autorecon2; then can we add control points at immediately after autorecon2 ? This way we would need to run autorecon3 only once and save resources. Or am I missing something and is it that one must run -autorecon2 and -autorecon3 and then add control points and then run -autorecon2-cp and -autorecon3 again. Thanks Mehul

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volumetrics questions
by Rashmi Singh 14 Mar '13

14 Mar '13

Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different. I did longitudinal run using the two mprages from same subject, however then also the volumes show differences. May you please advise me what to do. Thanks, Rashmi

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Estimate of number of manual edits and time to complete in 100subject sample
by Schumman Resonance 14 Mar '13

14 Mar '13

This is a question for the FS community in general, I gather there is variability around this, but rather than an exact number and time, I was hoping for an estimate on how many scans would I expect to require manual edits(any of the check points recommended in the tutorials) as well as an estimate of the time it takes to go through them. For the sake of the argument, take a sample of 100 subjects. Thanks, Kev

3 2

Permission denied
by Varghese Chikku 14 Mar '13

14 Mar '13

Dear FS team, I dowloaded the latest ML version of FS and tried to run a subject.But this error is coming up.Any suggestions? chikkuvarghese$ recon-all -i /Users/chikkuvarghese/Desktop/BL/raw/image00001 -autorecon-all -s BL1 mkdir: /Applications/freesurfer/subjects/BL1: Permission denied mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied cp: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer /Applications/freesurfer/subjects/BL1: No such file or directory. chikkus-MacBook-Pro:~ chikkuvarghese$

2 1

Stat doubts
by Gabriel Gonzalez Escamilla 14 Mar '13

14 Mar '13

2 1

convert from vtk to Freesurfer surface file format
by Christine Tardif 14 Mar '13

14 Mar '13

Hello, I would like to use the surface registration tools in Freesurfer. I first need to convert my vtk surfaces into the Freesurfer format. I tried mris_convert, but this seems to only convert from and not to the Freesurfer file format. Does anyone know of another conversion tool available? Thanks for your help, Christine. ___ Christine L Tardif, PhD Postdoctoral fellow Max Planck Institute for Human Cognitive and Brain Sciences Department of Neurophysics www.cbs.mpg.de/~ctardif

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Freesurfer March 2013