Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

-hippocampal-subfields-T1T2
by Daniele Orlandi 15 Jun '16

15 Jun '16

Dear All, I'm trying to run the flag -hippocampal-subfields-T1T2 with the new FS v6.0 but I get the following error: >Fitting mesh to synthetic image from ASEG took 217.8633 seconds >Transforming points >Transforming points >ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta): can't open file >No such file or directory >ERROR: Reading transform from file /media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta Do you have any suggestion? thank you all for your collaboration Daniele _______________________________________________________________________________ Daniele Orlandi, PsyD, Research Assistant Laboratory of Epidemiology, Neuroimaging Alzheimer IRCCS Centro San Giovanni di Dio, Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel:+39 030/3501563 cell: +39 3495119685 <%2B39%20030%2F3501563> email: dorlandi(a)fatebenefratelli.it; daniele.orlandi.psy(a)gmail.com (http://www.centroalzheimer.org/sito/chi_staff_e.php)

3 2

labels
by Trisanna Sprung-Much 27 Apr '16

27 Apr '16

Hi there I have two questions regarding using the labels with tksurfer: 1. What exactly has been done to change the .label (e.g. lh BA44.label) to .thresh.label (e.g. lh BA44.thresh.label? 2. The instructions on this page https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps to overlay the labels and set the Min and Max do not seem to work for me - I cannot seem to alter the Min from 2 and the Max from 5. Any thoughts as to why? thanks very much! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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AAL 3D rendering with subcorticals
by João V. Dornas 21 Apr '16

21 Apr '16

Dear friends, I am following this procedures to plot a 3D rendering of the AAL volume (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27707.html) My problem is the following. When I execute this command: mri_cor2label --i lh.Colin27_aal2std.mgh --id 75 --l lh_Pallidum_L specifically for the ROI Pallidum, a subcortical ROI, I receive the following error $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri lh.Colin27_aal2std.mgh Loading /Applications/freesurfer/subjects/FS_spm_CanonicalBrain/surf/lh.white Scanning the volume Found 0 label voxels ERROR: found no voxels matching id 75 This happens both for Pallidum Left and Pallidum Right, but all other AAL ROI work fine. I have an almost complete 3D rendering for my AAL. Only these subcortical regions are missing. Someone knows what could be happening? Thanks for the help. best, -- João V. Dornas Phd student in Neuroscience Cognitive Biology Group, Institute of Biology Otto von Guericke University, Magdeburg Germany

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DODS vs DOSS for correlation analysis
by Cassandra Wannan 13 Apr '16

13 Apr '16

Hi Doug, I am carrying out some correlations between cortical thickness and cognitive ability, and had a question about the use of DODS vs DOSS for my analysis with Qdec. From reading some of the forums, it seems as though DOSS should be used when there are no interactions present. I am including gender as a covariate (fixed factor) and age as a nuisance variable in my model. When I run this with DODS, it shows that the correlation between thickness and cognition does not differ between males and females - does this mean that I should run the correlation using DOSS? I only seem to find significant correlations using DOSS, however I do not want to report these if the analysis is not correct. Thanks, Cassie Cassandra Wannan *PhD Candidate/Research Assistant/Psychology Tutor* Melbourne Neuropsychiatry Centre -------------------------------------------- 0433 339 839 cwannan(a)student.unimelb.edu.au

5 12

3T or nuintensitycor3t
by Kasper Jessen 12 Apr '16

12 Apr '16

Dear freesurfer, To clear up som confusion i would like to ask if there is a difference between adding a -3T or -nuintensitycor3t flag? Best regards, Kasper -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j(a)cnsr.dk eller kasper.jessen(a)regionh.dk

2 3

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

2 5

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

2 1

Regarding: oblique view
by Dr Sampada Sinha 08 Apr '16

08 Apr '16

Dear freesurfer experts, Does adding an oblique angle during coronal or axial acquisitions of T1w images lead to topographical errors during mri_fix_topology process? Thanks and regards, Sampada -- Sampada Sinha

2 16

mris_fix_topology with ROI surface
by Ajay Kurani 06 Apr '16

06 Apr '16

Hi Freesurfer experts, I wanted to create a Freesurfer surface on some of the aseg ROIs. I was able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere some of the subcortical volumes for creating a surface. The mri_sphere had a big chunk that was deleted and so I wanted to run mris_fix_topology to fix this issue. In trying to run this command it appears that mris_fix_topology tries to correct based off of a brain sphere (which this ROI is clearly not) and therefore it fails. I plan to then run subsequent steps such as mris_euler number and mris_remove_intersections 1) Is there any way to fix the topology of this ROI using freesurfer tools or a way to work around this issue? Do you feel the sphere is needed for a small subcortical surface (ie globus pallidus) or is this really more for complex structures such as cortical surfaces? 2) Is there a recommended set of steps to accomplish creating a surface from the ROI that is different from what I stated? Thanks, Ajay

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Freesurfer March 2016