Freesurfer

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30131 discussions

manual talairach details
by Deane Aikins 15 Jun '09

15 Jun '09

Hello, I had a Talairach QA check failure, with the error log indicating a Z = -8 which was below the criterion of z =-6. I then used tkregister2 to attempt a manual alignment (no surf orig was available). After visual inspection, the subject and Talairach volumes looked really closely aligned already. I did some very conservative rotation and movement in the sagital plane, checked other planes, hit "SAVE REG" and then executed recon-all -all -subjid MYFILENAMEHERE in the subj directory. I then get the same error, with the same z score. I've tried several alignments (very little adjustment each time) with the same results. I notice that when I hit SAVE REG there is a new 4 x 4 numerical matrix written to my xterm screen. The values look very very similar to those prior. Is there a way to interpret these values to assist me in my manual alignment? Should I just bag it and use -notal-check? The majority of my patient set ran without errors. Thank you! Deane Aikins, PhD Director, Cognitive Neuroscience Laboratory National Center for PTSD Clinical Neuroscience Division Assistant Professor, Department of Psychiatry Yale School of Medicine

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Re: Freesurfer Digest, Vol 62, Issue 53 (fwd)
by Narly A Golestani 15 Jun '09

15 Jun '09

Hi there, I have a question regarding the longitudinal processing stream in the new release. I've already analyzed my data at different time points using the cross-sectional processing stream using the previous version of freesurfer, and would like to know if this is the same as doing so with the new release (or do I need to redo this). In a previous email I was told that I may have to rerun one step of the recon-all cross-sectionally (mri_ca_label step). If this is the case how can I go about re-running just this one step? Do I not need to also re-run all the steps following this as I assume that the next processing steps build upon the previous steps in the pipeline? thanks and best wishes, Narly. On Fri, 1 May 2009, Bruce Fischl wrote: > yes, although there is once piece that you'll need to rerun > cross-sectionally (I think just the mri_ca_label step)

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RES: [Freesurfer] qdec start
by ppj＠netfilter.com.br 15 Jun '09

15 Jun '09

Jose. 1) Yes. You should run -qcache 2) Yes. This file is used to describe your experiment. You can have more details in the FreeSurfer tutorial for group analysis. PPJ -- Pedro Paulo Jr E71 Nokia -----Msg original----- De: Jose Soares Enviada: 15/06/2009 06:38:02 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] qdec start Hi all, I am starting with qdec and i have a simple question. I have 30 recon-all subjects but I didn't do the -qcache option. 1- I want to know if I need to run this -qcache option even if I use the fsaverage target subject, or this is only necessary if se my own average subject? 2- Where do I make the connection between my subjetcs and qdec? It is only in qdec.table.dat? Thanks for the help, Miguel. Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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qdec start
by Jose Soares 15 Jun '09

15 Jun '09

Hi all, I am starting with qdec and i have a simple question. I have 30 recon-all subjects but I didn't do the -qcache option. 1- I want to know if I need to run this -qcache option even if I use the fsaverage target subject, or this is only necessary if se my own average subject? 2- Where do I make the connection between my subjetcs and qdec? It is only in qdec.table.dat? Thanks for the help, Miguel. Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Re: [Freesurfer] exporting surface as an image volume
by Mayuresh Korgaonkar 14 Jun '09

14 Jun '09

Hi Bruce, Thanks for your reply. I was planning on doing 1. voxel based statistics with our data in SPM, and 2. Overlaying the thickness data in original subject space. But I realised I could do the same statistics using Qdec. I had a few naive questions/clarifications about the ascii file generated for thickness, inflated and sphere surfaces. 1. The order of vertices in each of these files is the same? i.e. row 3 in thickness file should represent the same point on row 3 in the inflated and sphere files. 2. My understanding is that the coordinates are in the RAS space in each of the files? 3. The coordinates in "sphere.reg" file are in some average space? Is this MNI space? This would mean that the same coordinate in the sphere.reg files of different subjects represent the same anatomical area, right? Best regards, Mayuresh --- On Thu, 11/6/09, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] exporting surface as an image volume > To: "Mayuresh Korgaonkar" <mayureshkorgaonkar(a)yahoo.co.in> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Date: Thursday, 11 June, 2009, 8:45 PM > Hi Mayuresh, > > what do you want to do with it in SPM? The thickness > can be converted to > a volume format, but it will actually be a 1 x n vector, > where n is the # > of vertices in the surface. Not sure if that will be useful > or not. For > example from the surf dir you could do: > > mris_convert -c thickness lh.orig lh.thickness.mgz > mri_convert lh.thickness.mgz lh.thickness.nii > > to create a niftii file > > cheers > Bruce > > On Thu, 11 Jun 2009, Mayuresh Korgaonkar wrote: > > > > > > > Dear Freesurfer users and authors, > > > > Is it possible to export a surface (eg. ?h.thickness) > to an image volume - something which could be read into > SPM? > > I came across mri_surf2vol function, however I am not > to familiar with the usage. I understand that a volume > registration file is required, what exactly is this file? If > anyone can suggest an example usage of mri_surf2vol that > will be very helpful. > > > > Thanks in advance, > > Mayuresh > > > > > > Explore and discover exciting > holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/ > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/

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Details about aseg Stats
by Sherri Novis 11 Jun '09

11 Jun '09

Hello - can anyone tell me where I can find details on what aseg stats include and exclude from each measurement? The ones I need in particular are: Left-Cerebral-White-Matter Left-Cerebral-Cortex and IntraCranialVol. I'd like to understand if L-Cereb-Cortex means just gray matter, and/or if it includes ventricles & subcortical structures. I'm also trying to find out if IntraCanial Volume means the space of the skull cavity, or if it means something different. Thanks much in advance - Sherri

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total gray and white matter volumes, and total brain volume
by Dana W. Moore 11 Jun '09

11 Jun '09

Hi all, I am calculating total gray and white matter volumes using mrs_volume and mris_wm_volume, and I wanted to clarify what these are measuring. I am following the instructions on the morphometry stats wiki page, which say to use mris_volume and subract wm from pial volume to get total gray matter. Will this leave me with all gray matter including cortical and subcortical? Then I use mris_wm_volume to calculate total wm. Again, does this include all white matter in the brain? Also, what would be the best way to calculate total brain volume? I could add the calculations for gray matter and white matter described above, or I could use BrainSetNotVen from the aseg stats file, or I could add all the structures in the aparc and aseg files. Any recommendation on which is best? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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(no subject)
by Sally Bernardina Seraphin, PhD 11 Jun '09

11 Jun '09

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[FSL] Social event for Iranian Neuroimagers (fwd)
by Bruce Fischl 11 Jun '09

11 Jun '09

FYI ---------- Forwarded message ---------- Date: Thu, 11 Jun 2009 16:27:15 +0100 From: Mojtaba Zarei <mojtaba(a)FMRIB.OX.AC.UK> Reply-To: FSL - FMRIB's Software Library <FSL(a)JISCMAIL.AC.UK> To: FSL(a)JISCMAIL.AC.UK Subject: [FSL] Social event for Iranian Neuroimagers Dear All, I am trying to arrange a social event for Iranian Neuroimagers during HBM in San Francisco. Could anybody who is interested contact me please (with or without suggestion)? Kind regards, Mojtaba Zarei PS: Apologies for using this email list ...

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exporting surface as an image volume
by Mayuresh Korgaonkar 11 Jun '09

11 Jun '09

Dear Freesurfer users and authors, Is it possible to export a surface (eg. ?h.thickness) to an image volume - something which could be read into SPM? I came across mri_surf2vol function, however I am not to familiar with the usage. I understand that a volume registration file is required, what exactly is this file? If anyone can suggest an example usage of mri_surf2vol that will be very helpful. Thanks in advance, Mayuresh Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/

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