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30132 discussions

BOLD vol2surf dimension mismatch
by Linda Douw 10 Aug '12

10 Aug '12

Hi all, I'm trying to project volume BOLD time series to native surface in some subjects. First, I registered the functional data to orig.mgz, using: bbregister --s subj --mov func.nii.gz --reg register.dat --init-fsl --bold --o output.nii.gz The results look good in tkregister2. Then, I want to go from volume to surf, doing: mri_vol2surf --mov functional.nii.gz --reg register.dat --regheader nmr00524_FS --hemi lh --o /folder/ However, it gives this error message: Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 26361 Writing to /folder/ Dim: 132698 1 1 non-standard value for imnr1 (1, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (132698, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure I should probably use mri_vol2vol first, but which target volume should I then use? Or is there something else I'm doing wrong? Thanks for your help! -- 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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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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