Freesurfer

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30084 discussions

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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Regarding: Group analysis of WMHs
by Dr Sampada Sinha 08 Apr '16

08 Apr '16

Dear freeesurfer experts, I am trying to calculate WMHs of MDD patient populations. I ran the T2FLAIR separately after processing T1 with recon-all. Presently, I don't have any dwi data where I can project the WMHs onto the WM tracts. Will you please tell me how do I project the WMHs of 29 MDD patients on a template (?) showing the WMH abnormalities? Or if you can please recommend a paper or freesurfer page from where I can get a step by step directions of showing WMHs of 29 cumulative MDD patients on subcortical surface. Thanks and regards, Sampada -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India

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Qdec DOSS
by tom parker 08 Apr '16

08 Apr '16

Hi Freesurfers, I posted this question a few days ago but didn't get any replies. Would you mind answering this for me? I compared 2 groups, while controlling for 1 covariate in qdec using freesurfer 5.1. There were no significant interactions with the covariate so I need to use DOSS. I read on several post that DOSS has some bugs related to the generation of contrasts in qdec and that mri_glmfit should be used to run a DOSS analysis. However, when I ran my analysis with DOSS in qdec I saw that the C.mat file looked like this: 1 -1 0, which seems correct to me. My question is can I use DOSS in qdec in this case? Or are there other bugs related to using it in qdec? Thank you so much!

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Re: [Freesurfer] errors on the WM and Gray inflated surfaces
by pablo najt 08 Apr '16

08 Apr '16

Dear FS expert and users,We are coming across errors on the WM and Gray inflated surfaces.When trying to open the surfaces with tksurfer as follows (tksurfer subid lh inflated -gray) We get only a small part of the cortex displaying. Also when we try file-label-import annotation the following error occurs:colortable with 13 entries read (originally /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt)Found embedded color table in annotation. There seem to be no hard failures as recon-all log said "finished without errors". Also WM and pial surfaces look accurate.Now we are trying to figure what is that could have caused this for all subjects.We have an old instructions for freesurfer saying to to run recon-all as follows.run recon -all -s subjID /autorecon -all As I am not familiar with this way of running recon-all I wanted to ask if this could have caused the problem consistently across 70~ subjects.Any advise on this would be greatly appreciated.Cheers.Pablo

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