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17 participants
30086 discussions

mri_preproc
by shinjini＠andrew.cmu.edu 08 Sep '14

08 Sep '14

Hi, I couldn't find the documentation for mri_preproc. I know that roughly it resamples multiple subjects' brain images into the same space and then concatenates the vertices, but I want to know details like: Exactly how are the brains resampled? What is the procedure beyond the Talairach affine and spherical registration steps? Individual brain images have different numbers of vertices. Which vertices are chosen overall? How are they chosen? How is correspondence between a single vertex location across all the images established? Is the finite element approximation and vertex selection procedures invariant? Do they yield the same set and location of vertices despite minor variations? Under what conditions are they invariant? After the vertices are obtained how are they concatenated? Are they listed in a particular order and is this order the same for all the brains? How is the order determined? Thanks in advance for your reply, ~Jen

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Qdec question
by Abrishamchi, Aurash David 08 Sep '14

08 Sep '14

Hello, I still cannot solve this issue. All help will be appreciated. I am running Qdec analysis on about 100 subjects and correcting with FDR. Once I do this I click the "find clusters and go to max" button and Qdec gives me a plot of all the data as well as taking me to the max vertex in the #1 cluster. I want to extract the data from the table so that I can put it in excel and calculate some correlations however I cannot find a way to do so without hovering or clicking on each data point and manually entering the values into excel. As you can imagine this is very tedious when there are 100 subjects and 12 regions that we are looking at. Please let me know if there is an alternative way to export the data into excel or even to a word processing file so that the values can be copied and pasted into excel. Best, Aurash Abrishamchi Research Co Op - NCRI - Massachusetts General Hospital 165 Cambridge Street, Suite 600 Boston, MA 02214 P: 617-726-4284 AAbrishamchi(a)mgh.harvard.edu

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Manual editing compared to non-manual editing.
by Kasper Jessen 08 Sep '14

08 Sep '14

Hi, Thank you for a good freesurfer course in Copenhagen. After the course i have been wondering if there is available litterature regarding manuel editing versus non-manuel editing? Has any studies investigated the outcome/results from manual editing versus non-manuel editing on the same sample of subjects? Best regards, Kasper Jessen

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Difference between surfcluster and volcluster
by Katharina Zech 08 Sep '14

08 Sep '14

Dear all, I run the surfcluster analysis (mri_surfcluster). But the tutorial tells me that there exists also mri_volcluster: Using the outputs from the estimation step and the simulations, mri_surfcluster (or *mri_volcluster*) will create two outputs: the summary file with a table of the clusters it found, and an output surface map of the clusters wth the cluster-wise p-value. The sample mri_surfcluster command is: mri_surfcluster --src lh.gender_age.glmdir/age/sig.mgh \ --csd lh.gender_age.glmdir/csd1-age.csd \ --csd lh.gender_age.glmdir/csd2-age.csd \ --sum lh.gender_age.glmdir/age/sig.cluster.sum \ --ocp lh.gender_age.glmdir/age/sig.cluster.mgh Could you please tell me the difference between surfcluster and volcluster? How do I have to change the preprocessing steps mris_preproc, smoothing (surf2surf), mdi_glmfit and the simulation to get volcluster instead of surfcluster? Thanks in advance! Katharina

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Re: [Freesurfer] Cortical gray matter surface area
by will brown 08 Sep '14

08 Sep '14

Sorry, my mistake. I did mean surface area rather than volume. I am unsure as to how to find the total surface area of the cortical gray matter as ?.aparc.stats file only report WhiteSurfArea. Thanks, Will Message: 17 Date: Wed, 27 Aug 2014 00:48:29 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cortical gray matter surface area To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <53FD631D.4070608(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" The volume for each structure is given as the 4th column. If you want total GM volume, look in aseg.stats doug On 8/26/14 8:43 PM, will brown wrote: > Hi all, > > I am a little unclear as to how to find the cortical grey matter > volume in the stats output files. The ?.aparc.stats file shows: > > Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2 > > What about grey? > > Thanks, > Will

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seed-based functional connectivity: mkcontrast-sess
by Robby De Pauw 08 Sep '14

08 Sep '14

Dear FreeSurfer community, I was wondering what my contrast-matrix should look like when doing a first-level analyses since there is no task involved. I tried looking at the -help flag, but I can’t see any options for setting a matrix without entering the numb of conditions. This was the command I tried to use: mkcontrast-sess -rmprestim -analysis restingstate.sm05.lh -contrast restingstate.lh I’m sure I’m missing something here, but I can’t figure out what to do. Thanks for the already given support!! Best regards, Robby Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent Robby.DePauw(a)Ugent.be

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Freesurfer at 7T
by Lucy Hiscox 07 Sep '14

07 Sep '14

Dear Freesurfer experts, I am currently trying to segment a 7T image at 0.8 isotropic resolution. I have an MPRAGE scan and a Gradient echo, and want to coregister the data before processing to correct for inhomogenities, but unsure whether I can use FSL instead of SPM. I am following these instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon I am new to SP8 and not sure what I would have to do with this information specifically: (i1./i2 .* (i2>20)) .* 100. Also, is it possible to just use the recon-all process or would you recommend going through each step individually outlined above? Is the second option the option for keeping the voxels at 0.8? Furthermore, I read somewhere that you have to use the -cm -aseg command to keep the voxels the same. is this true? Best wishes and many thanks, Lucy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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about issues with "recon-all"
by Abel Lei 06 Sep '14

06 Sep '14

Hi FreeSurfers, I’m a very beginner to both the Linux OS and the FreeSurfer program. After finally setting up the FreeSurfer, I was trying to do recon-all for my trial subject. But when I ran the “recon-all” command, it returned with a long error message indicating many commands not found. The message is copied and pasted below. I also attached the recon-all.log and recon-all.error in this email, which (probably) contains two failed attempts of the same command. Please let me know if you need any other info from me. I appreciate your help and time greatly! Thank you so much! Chia-Ming (Abel) Lei PhD Student/Graduate Student Researcher Language and Brain Lab (LABlab) & Adult Language Lab Department of Communication Sciences and Disorders School of Health and Rehabilitation Science University of Pittsburgh -----below is the long~ error message------ chiaming-PORTEGE-R835:~> recon-all -all -s mike_dickeySubject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot Actual FREESURFER_HOME /home/chia-ming/Desktop/freesurfer -rw-rw-r-- 1 chia-ming chia-ming 2119 Sep 6 01:34 /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/scripts/recon-all.log Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux mri_motion_correct.fsl: Command not found. talairach_avi: Command not found. tkregister2_cmdl: Command not found. nu_correct: Command not found. mri_make_uchar: Command not found. mri_normalize: Command not found. mri_watershed: Command not found. mri_gcut: Command not found. mri_segment: Command not found. mri_label2label: Command not found. mri_em_register: Command not found. mri_ca_normalize: Command not found. mri_ca_register: Command not found. mri_ca_label: Command not found. mri_pretess: Command not found. mri_fill: Command not found. mri_tessellate: Command not found. mri_concatenate_lta: Command not found. mri_normalize_tp2: Command not found. mris_smooth: Command not found. mris_inflate: Command not found. mris_curvature: Command not found. mris_sphere: Command not found. mris_fix_topology: Command not found. mris_topo_fixer: Command not found. mris_ca_label: Command not found. mris_euler_number: Command not found. mris_make_surfaces: Command not found. mris_register: Command not found. mris_volmask: Command not found. mris_anatomical_stats: Command not found. mrisp_paint: Command not found. mris_curvature_stats: Command not found. mris_calc: Command not found. mri_robust_register: Command not found. mri_robust_template: Command not found. mri_and: Command not found. mri_or: Command not found. mri_fuse_segmentations: Command not found. mri_segstats: Command not found. cp: cannot stat 'Desktop/freesurfer/bin/recon-all': No such file or directory #-------------------------------------------- #@# MotionCor Sat Sep 6 01:40:13 EDT 2014 ERROR: no run data found in /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/mri. Make sure to have a volume called 001.mgz in /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s mike_dickey exited with ERRORS at Sat Sep 6 01:40:13 EDT 2014 For more details, see the log file /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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LGI Topological Defect
by Tara Miskovich 06 Sep '14

06 Sep '14

Hi all, I am getting an error that seems common for people running LGI where it crashes due to a topological defect. I have run mris_euler_number and everything looks fine. Plus, I went through each slice and made sure the surfaces looked good. Any advice on any other steps I can take? I have already tried rerunning recon-all. Thank you! Tara

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Re: [Freesurfer] tracula: bvec-error
by Robby De Pauw 05 Sep '14

05 Sep '14

Hi Anastasia, I’m using this version of tracula. trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp I’ve attached the log-file you requested. Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent Robby.DePauw(a)Ugent.be

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