Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 discussions

mri_glmfit DOF error
by matteo.diano＠tiscali.it 08 Jul '11

08 Jul '11

Hello Freesurfers, I have a problem with mri_glmfit. I performed the analysis on two FA data. My fsgd is: GroupDescriptorFile 1 Title SUBJ_FA Class PRE Class POST Input FA_1 PRE Input FA_2 POST group_difference.mtx: 1 -1 The results in cmd line DOF = 0 ERROR: DOF = 0 What does it mean this error? Thank you for your help. Matteo Non temiamo alcun confronto: Tiscali ha l'Adsl più veloce d'Italia!Risparmia con Tutto Incluso Light: Voce + Adsl 20 mega a soli 17,95 € al mese per 12 mesi.http://abbonati.tiscali.it/telefono-adsl/prodotti/tc/tuttoincluso_light/?WT.mc_id=01fw

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Re: [Freesurfer] Freesurfer and VBM
by Ed Gronenschild 08 Jul '11

08 Jul '11

Hi Fatima, Your findings are not surprising. There is plenty of literature describing problems with the VBM technique. You may read e.g., Kennedy et al (2009), Neurobiology of Aging, vol. 10, 1657-1676 and references cited herein. Ed On 8 Jul 2011, at 15:02, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Hello, > > I'm wondering if anyone could help me out with a question I had. For > a study I'm working on, I'm comparing the regional brain volumes in > adolescents with and without PTSD. I ran VBM analysis and Freesurfer > on my subjects and I found some significant results on VBM (however, > only using uncorrected p values) and on Freesurfer, I found no group > differences in brain regions. Is there an explanation for that? > > If anyone has any thoughts I'd really appreciate it. Thank you kindly! > > Fatima

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make_average_subject error
by leonardo kay 08 Jul '11

08 Jul '11

Hi all Could anyone help me with this error: MRISreadAnnotationIntoArray: vertex index out of range: 1499028058 i=5A595959, in_array_size=133467 annot file: /home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot This appeared after trying to average my subject data. It says ' vertex index out of range '. All acquisitions were made using the same parameters so I don't know what this may mean. Thanks in advance -- Leo Kay.

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A question about the Freesurfer version compatibility of Tracula
by Shanqing Cai 08 Jul '11

08 Jul '11

Hi, I am using Tracula, a new tool that comes with version 5.1.0 of FreeSurfer. However, my data set are processed with the recon-all of an earlier version of FreeSurfer: 5.0.0. I wonder whether I need to rerun recon-all on all the subjects in the data set with 5.1.0. Would running Tracula on 5.0.0 reconstructions cause any problems that render the results unusable/not trustable? Thank you! Best, Shanqing Cai

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Retinotopy stimuli
by Anders Hougaard 08 Jul '11

08 Jul '11

Dear freesurfers, Which stimuli do you think provide the best retinotopic maps? I have done a retinotopy analysis using the following stimuli: Polar angle: - 45 deg counter-clockwise rotating wedge - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Eccentricity: - expanding ring - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Any suggestions on how to optimize this stimulation? E.g. different period length, more runs, bi-directional, different TR Thank you! Best regards, Anders

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FreeSurfer use in dogs
by Marjorie Milne 08 Jul '11

08 Jul '11

Hello Freesurfers, I would like to use FreeSurfer to analyse brain morphology in dogs but do not know if the techniques can be applied in this species. Does anyone have experience using FreeSurfer in dogs, and any tips to get the techniques to work? Regards, Marjorie Milne

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question about qdec
by ZhiLiangLong 07 Jul '11

07 Jul '11

Hi all: I have three groups of subjects (major depression disorder,slight depression disorder and contrast),i want to use qdec to obtain the statistical significant areas containing difference of cortical thickness measurment among them. But there are some errors appearing when i run the group analysis: ERROR: QdecGlmDesign::GenerateContrasts: factor 2 must have 2 levels I think the error is related to the diagnosis.levels file which has 3 levels because i can run it successfully after removing any one of them.But i don't know why. Can you give me some help or suggestions? I have saved error information into the error.log file(see attachments)

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more on fieldsign problems-
by Michelle Umali 07 Jul '11

07 Jul '11

Dear all, I've been having issues with my fieldsign images all I get are speckles. I did the following and did not get any errors: 1) ran recon-all -all 2) cut and saved occipital patches (rh.occip.patch.3d) from inflated surface 3) ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d rh.occip.patch.flat 4)mkanalysis-sess -rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 paradigm rtopy.par -nskip 4 fwhm 0 5) selxavg3-sess -a rtopy.self.rh -s sj09 6) fieldsign-sess -a rtopy.self.rh -occip -s sj09 When I looked at the fieldsign map using: 7) tksurfer-sess -a rtopy.self.rh -s sj09 -fieldsign all I got were blue and red speckles. The polar and eccentricity maps seemed ok. Any help would be great. Michelle

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preprocessing qc
by Chindhuri Selvadurai 07 Jul '11

07 Jul '11

Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

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Re: [Freesurfer] Error with Tksurfer
by Bruce Fischl 07 Jul '11

07 Jul '11

Hi Antonella, did bert inflated look ok on the other computer? Usually this problem goes away if you update the video card driver. cheers Bruce On Thu, 7 Jul 2011, Antonella Kis wrote: > Good afternoon Bruce, > > I am still trying to fix my error related to the surface image display when using tksurfer bert lh inflated. As you saw the image looks weird and what I in the mean time I > tried something: I save the weird surface displayed by that computer using SAVE SURFACE AS and I transfers this file nsmed by me lh.bertsurf to another computer. When I > looked on the image using > tksurfer bert lh bertsurf, the surface that came up was exactly like the bert lh inflated should be, having the same number of vertices and faces. Can you or somebody else > give me some advice on what to do so I can get the same display on the other computer? Seems that everything is well calculated just the surface display/image is looking > weird on that computer. What can be the problem? I attached the saved surface from the computer where it looked weird so the called "weird surface". > > Also can I save a surface and loaded in freesurfer but not as a tiff image? What's the best way to save my volumes and/or surfaces? > > Thank you very much for your help. > Antonella > > > > >

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Freesurfer July 2011