Freesurfer August 2012

freesurfer@nmr.mgh.harvard.edu

110 participants
170 discussions

Re: [Freesurfer] WM-hypointensities
by Mary Ellen Koran 10 Aug '12

10 Aug '12

Hi, I'm responding to this archived email: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/023599.html Is it possible to run recon-all with the switch -nowmsa to get rid of the white matter segmentation analysis? Thanks! > > Mary Ellen Koran > MD/PhD Candidate, MSTP > Thornton-Wells Lab, Center for Human Genetics Research > Vanderbilt University School of Medicine > Duke University, Class of 2009, BSE > Cell: 919.943.5114 > >

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Tracula question
by Natalia Sánchez 10 Aug '12

10 Aug '12

Hi! I am running tracula for the first time and I am encountering the following error: Loading brain mask of output subject from /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain_mask.flt.nii.gz niiRead(): error opening file /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain_mask.flt.nii.gz Loading FA map of output subject from /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_FA.flt.nii.gz niiRead(): error opening file /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_FA.flt.nii.gz Segmentation fault Darwin dhcp-165-124-9-95.phystherapy.northwestern.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Fri Aug 10 16:19:17 CDT 2012 what file is lowb_brain_mask.flt.nii.gz? should this have been created during tracula or is this file my nodiff image? Thanks! *-- Natalia Sánchez * PhD Candidate Departments of Biomedical Engineering & Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611

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mri_convert downsample then resample shifts image upward one voxel
by Joshua Lee 10 Aug '12

10 Aug '12

I used mri_convert to resample my norm.mgz to 0.25 mm iso nii.gz, and then again back up to 1mm isotropic space. The resultant image shifted up a voxel from the original converted straght to nii.gz. This points to the resampling procedure, and not the conversion to different file format. Suggestions? Note: I wanted to hand trace the hippocampus in the norm.mgz, and upsampled the norm.mgz to trace on. I traced it, and then downsampled to 1mm to compare with Freesurfer segmentation, but found it shifted. Josh

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Re. QDEC results
by Gibbard, Clare 10 Aug '12

10 Aug '12

Hi Doug, Thanks for your quick response - that all makes sense now. Best wishes, Clare ------------------------------ Message: 13 Date: Fri, 10 Aug 2012 10:19:43 +0000 From: "Gibbard, Clare" <c.gibbard(a)ucl.ac.uk> Subject: [Freesurfer] QDEC results To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <D2ACCCB2F2AEDD40865D0836BF8D33B6224C82C9(a)DB3PRD0104MB131.eurprd01.prod.exchangelabs.com> Content-Type: text/plain; charset="iso-8859-1" Hello, I went on the FS course in Amsterdam recently. I have run a QDEC analysis to see whether cortical thickness differs between my two groups. I have two questions: 1. I put in the lh_bankssts_thickness as my continuous variable. The display outputs results for whether average thickness differs between my groups. The significant clusters appear in areas which are far away from the lh_bankssts. Is this correct? Does the design somehow look at overall cortical thickness in the lh even though I have only specified the lh_bankssts? 2. I can't see the button for controlling for multiple comparisons. From the wiki I believe this is supposed to appear under a scalar heading, but I can't see it. Do I need to add something in order to do this? Thank you very much. Best wishes, Clare ---------------- Message: 21 Date: Fri, 10 Aug 2012 11:03:52 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] QDEC results To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <502522D8.2080307(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Clare, On 08/10/2012 06:19 AM, Gibbard, Clare wrote: > Hello, > > I went on the FS course in Amsterdam recently. I have run a QDEC > analysis to see whether cortical thickness differs between my two > groups. I have two questions: > > 1. I put in the lh_bankssts_thickness as my continuous variable. The > display outputs results for whether average thickness differs between > my groups. The significant clusters appear in areas which are far > away from the lh_bankssts. Is this correct? Does the design somehow > look at overall cortical thickness in the lh even though I have only > specified the lh_bankssts? I think it is correct. You are not confining the analysis to bankssts. You are basically using bankssts as a nuisance variable. > > 2. I can't see the button for controlling for multiple comparisons. > From the wiki I believe this is supposed to appear under a scalar > heading, but I can't see it. Do I need to add something in order to > do this? You should not need anything else. Are you on the "Display" tab? It should be under the "Clusters" area. doug

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ico4 parcellation and mri_segstats
by Linda Douw 10 Aug '12

10 Aug '12

Dear Freesurfers, I'm trying to extract the average waveforms from all 2562 ROIs in an annotation constructed using mris_make_face_parcellation with ico4. However, I get only 2460 waveforms after doing mri_segstats, and the summary files show that several ROIs are 'skipped' for some reason. Am I missing something? Thanks, -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129

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Talairach registration
by Alexandra Tanner 10 Aug '12

10 Aug '12

Hi Doug, I'm currently looking into doing surface edits on past data and I heard someone mention that one should never scale the brain when editing the talairach registration. I was wondering if this was true, or if it's okay to scale the brain so long as you check the scaling in all 3 dimensions after doing so. Any input would be great! Thanks, Alex

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QDEC results
by Gibbard, Clare 10 Aug '12

10 Aug '12

Hello, I went on the FS course in Amsterdam recently. I have run a QDEC analysis to see whether cortical thickness differs between my two groups. I have two questions: 1. I put in the lh_bankssts_thickness as my continuous variable. The display outputs results for whether average thickness differs between my groups. The significant clusters appear in areas which are far away from the lh_bankssts. Is this correct? Does the design somehow look at overall cortical thickness in the lh even though I have only specified the lh_bankssts? 2. I can't see the button for controlling for multiple comparisons. From the wiki I believe this is supposed to appear under a scalar heading, but I can't see it. Do I need to add something in order to do this? Thank you very much. Best wishes, Clare ----------- Clare Gibbard PhD Student Imaging & BioPhysics Unit 4th Floor Institute of Child Health 30 Guilford Street London WC1N 1EH Tel. 020 7905 2192 Email: c.gibbard(a)ucl.ac.uk

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unable to download ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol
by Knut J Bjuland 10 Aug '12

10 Aug '12

HI I am unable to download ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol. Could you pleas add the file back. Knut J

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Freesurfer 5.2 or new trac_all
by Knut J Bjuland 10 Aug '12

10 Aug '12

When will FreeSurfer 5.2 be release. Is is possible to download the news version of trac-all and fsl_sub and use them in FreeSurfer 5. since I am using fsl 4.1.9. Knut Jørgen

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mri_vol2surf or mri_cor2label
by Stephanie Rossi 09 Aug '12

09 Aug '12

Hi, I have seeds defined in fsl for individual subjects (nii.gz) and I would like to convert them to freesurfer labels for individual subjects. Which command would I have to use: mri_vol2surf or mri_cor2label? Thank you for your help! Best, Stephanie

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Freesurfer August 2012