I did. This is what I get from my group analysis in the folder. I didn't find the ocn.dat file. Is there something I need to do in Qdec to produce it?
C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh cnr.mgh mc-z.abs.th13.pdf.dat mc-z.abs.th13.sig.vertex.mgh F.mgh mc-z.abs.th13.sig.cluster.mgh sig.mgh gamma.mgh mc-z.abs.th13.sig.cluster.summary gammavar.mgh mc-z.abs.th13.sig.ocn.annot
Thank you again for the help! Tara
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 8, 2013 10:48:10 AM Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Did you generate the annotation from a qdec analysis of lgi? If so, then there should be a file already there called something like mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for each cluster. The value will be the mean lgi for that subject and cluster. Is this what you need?
doug
On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote:
I see, could you help me go about this. I have not been able to figure out how to do this with an annotation file. And I believe I already mapped my lgi to fsaverage space before group level through recon-all -qcache. Is this what you mean?
Thank you again for the help! Tara
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Monday, October 7, 2013 1:59:37 PM Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Oh, you'll need to map the annotation into the individual space, or (and probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
Thank you Doug, this did work. However, for every subject I get this line repeated over and over before it outputs the stats. I still get a stats file that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=00000000, in_array_size=136201 annot file: ./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help! Tara
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, October 4, 2013 6:29:49 PM Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
This may sound incredibly trivial, but try putting a "./" infront of qdec, ie, "-a ./qdec/..."
doug
On 10/04/2013 03:42 PM, Tara Ann Miskovich wrote:
Hi Everyone,
I am having trouble running mris_anatomical_stats on an annotation file produced from my group analysis in qdec.
This is my code, but it seems to want to pull the annotation file from the subject/label directory. Should I just make a copy into everyone's label file?
mris_anatomical_stats -a qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot -t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats ${subject} lh
Thank you! Tara _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer