Freesurfer April 2016

freesurfer@nmr.mgh.harvard.edu

122 participants
173 discussions

From Talairach to Vertex Index
by Ilaria Mazzonetto 11 Apr '16

11 Apr '16

Hi FS users, I need to check if a specific point in Talairach coordinates is inside a label that I created from a significative cluster of a previous group analysis (the template is fsaverage). How can I do this quickly? Thanks a lot. Best regards. Ilaria

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$FREESURFER_HOME/sources.csh
by Marco Loggia 11 Apr '16

11 Apr '16

Good morning Doug and all, I am running epidewarp.fsl (using the dev version since I need it to be compatible with the recent versions of FSL; /usr/local/freesurfer/dev/bin/epidewarp.fsl). However, for the first time I see that it complains that it can no longer find /usr/local/freesurfer/stable5_3_0/sources.csh. How can this be fixed?? Thanks! Marco _______________________________________________________ Marco L. Loggia, PhD Assistant Professor of Radiology, Harvard Medical School Associate Director, Center for Integrative Pain NeuroImaging (CiPNI) A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 Email: marco(a)nmr.mgh.harvard.edu Web: http://scholar.harvard.edu/loggia

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Accuracy of D-K atlas for different age ranges
by Kirstie Whitaker 11 Apr '16

11 Apr '16

Hi Freesurfer community, A reviewer has asked how accurate the application of freesurfer regional labels are to different age ranges (specifically our study is between 14 and 24 years old). I'm sure this question has been answered elsewhere so please do forgive me for being lazy and simply asking you to recommend good references rather than searching for them in PubMed! Thank you! Kirstie x -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com

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TRACULA dev version: Error message
by Elijah Mak 11 Apr '16

11 Apr '16

Hi Freesurfer Community, I am running TRACULA on a single subject in the dev version (freesurfer-Darwin-OSX-stable-v6-beta-20151015) #------------------------------------- /Applications/freesurfer6beta/bin/trac-preproc #------------------------------------- #@# Image corrections Mon Apr 11 16:15:19 BST 2016 mri_convert /Users/MacPro/Documents/NIMROD_DTI/16084.nii.gz /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz mri_convert /Users/MacPro/Documents/NIMROD_DTI/16084.nii.gz /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ reading from /Users/MacPro/Documents/NIMROD_DTI/16084.nii.gz... TR=11700.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998406, -0.0447105, -0.0344521) j_ras = (-0.0435914, 0.998518, -0.0325768) k_ras = (-0.0358576, 0.0310231, 0.998875) writing to /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz... cp 16084.bvec /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvecs cp 16084.bval /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvals mv -f /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvecs.tmp /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvecs mv -f /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvals.tmp /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvals flip4fsl /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -8 fslswapdim /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz x y z /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.nii.gz mv -f /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.mghdti.bvecs /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvecs mv: rename /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.mghdti.bvecs to */Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvecs: No such file or directory* *trac-preproc exited with ERRORS at Mon Apr 11 16:16:26 BST 2016* --- What has gone wrong here? Thanks! Elijah

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Viewing eroded structure after -seg-erode 1
by Elijah Mak 11 Apr '16

11 Apr '16

Hi Freesurfer Community, I have performed -seg-erode 1 during mri_segstats on resampled subcortical strutures (T1 to FA/MD). Can I view the eroded masks in T1 anatomical space to visually inspect whether PVE has been adequately accounted for? Thank you. Best Wishes, Elijah

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stacked iteration in brainstem segmentation
by Claudia Testa 11 Apr '16

11 Apr '16

Dear all, I wrote few weeks ago for a problem regarding Freesurfer 6.0 and the -brainstem-structures option. The bug was solved downloading the new available version but I still have some problems. The recon-all -s subject -brainstem-structures stacks at a certain point (always the same one: "Iteration 2 of 7") for some subjects and for others it succeedes. In attach there is the log file for one successful segmentation (brainstem-structures_ok.log) and one for a failed segmentation (brainstem-structures.log). Can you help me? Thanks a lot Claudia 5x1000 AI GIOVANI RICERCATORI DELL'UNIVERSITÀ DI BOLOGNA Codice Fiscale: 80007010376

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(no subject)
by Josh Rutta 10 Apr '16

10 Apr '16

Hi, I’m new to freesurfer, I’m an undergraduate currently doing research involving analyzing mri scans to produce volume measurements of the hippocampus. I’ve been using FSL’s FIRST method to do this thus far, but from what I’ve read online, freesurfer is much better for volumetric analysis of subcortical structures. The problem is that I can’t seem to find a good step by step tutorial to use free surfer. Also I’ve noticed free surfer runs on omgz files, and I’m dealing with nii files. I’d appreciate it if I could a step by step list of instructions on: 1) How to convert the nii files to mgz files correctly 2) getting volume of hippocampus from an mri scan I appreciate the help, thanks! Josh

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Left right flip surfaces
by Ajay Kurani 08 Apr '16

08 Apr '16

Hello Freesurfer Experts, I processed all of my brains through freesurfer 6.0 dev for Linux and warped the surfaces to standardized space. For a handful of subjects I want to perform a left right flip of the cortical thickness files (standardized space) for a group analysis. What is the best way to perform this in freesurfer? I have found a previous post referencing mris_reverse but there was a mention of it being off by a voxel when flipped. I wanted to see if this is still a concern with the latest version? Is there a better way to achieve this goal without rerunning all of freesurfer such as a newer took, or is this the preferred method? Thanks, Ajay

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binary mask for the gm wm and csf
by Mohamed Ali Bahri 08 Apr '16

08 Apr '16

Dear Freesurfer experts, I am wondering if the gm/wm/csf binary masks (with of course the cerebellum) could be extracted from the recon-all freesurfer results. Any idea/suggestion will be very welcome. Many thanks in advance, Best regards, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri(a)ulg.ac.be

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asegstats2table list index out of range
by Lars M. Rimol 08 Apr '16

08 Apr '16

Hi, I'm trying to run asegstats2table asegstats2table --subjects subjlist.csv --skip --delimiter comma --common-segs --tablefile asegs_03042016.csv All subjects in the subjlist are present in the directory but I get this error message: Parsing the .stats files Building the table.. Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 560, in <module> rows, columns, table = sanitize_table(options, pretable) File "/usr/local/freesurfer/bin/asegstats2table", line 454, in sanitize_table _specs, _id_name_map, _measl = _t[0] IndexError: list index out of range I get the error message even if I reduce the list to two subjects. It works if I do this (all subjdirs begin with PD): asegstats2table --subjects PD* --skip --delimiter comma --common-segs --tablefile asegs_03042016.csv And it works if I enter the subjects' names individually. With over 100 subjects, however, that's not an option. I'd be grateful for any suggestion on how to run asegstats2table with a subjects list. Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Freesurfer April 2016