Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Re: [Freesurfer] Annotation question
by Douglas N Greve 08 Mar '12

08 Mar '12

Hi Antonella, use cvs_avg35 as the subject and ?h.aparc.annot for the annotation. Antonella Kis wrote: > Hi Doug, > > Sorry I bother again I just want to ask you an advice. I was running > the code which was sent to me by Don: > > vals = fs_tal2surf([-16.92 -29.55 34.44]); > ind_lh = find(vals{1}); > ind_rh = find(vals{2}); > > [lh_roinums,lh_roilabels] = fs_read_annotation(fname_annot_lh); > [rh_roinums,rh_roilabels] = fs_read_annotation(fname_annot_rh); > > if ~isempty(ind_lh) > roinum = lh_roinums(ind_lh); > roilabel = lh_roilabels{roinum}; > elseif ~isempty(ind_rh) > roinum = rh_roinums(ind_rh); > roilabel = rh_roilabels{roinum}; > end > > > and it works perfect but I am a little confused regarding my data. > > I am looking to find the nearst cortical label for my clusters for the > DTI data:FA, MD,RD,AD. I registered this data on the CVS space so I > wonder if I should use for the fname_annot_lh and fname_annot_rh the > annotations from the CVS space not from fsaverage. I tried both and > got different locations for my clusters. > > Can you please advise me? > > Many thansk. > Antonella -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Interpreting Results
by Allie Rosen 08 Mar '12

08 Mar '12

Hi All, I'm having trouble reconciling the cluster colours with the graph that can be made when you load the group descriptor file and click on a point. I've attached an example. In this study, I'm comparing thickness in a patient and control group, with age regressed out. The contrast I've used means that blue means control<patient. Therefore, patients are thicker than controls. But in the graph, patients don't seem to be thicker. I've seen the same results with red clusters (i.e. they should mean that controls are thicker but the graph shows otherwhise). Please let me know how I can interpret my findings given the graph. Which group is actually thicker? Thank you, Allison

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Re: [Freesurfer] aparc.a2005s+aseg.mgz
by Douglas N Greve 08 Mar '12

08 Mar '12

Hi Mark, I don't think thalamic structures were part of the a2005s. I think it was only cortical structures. The aparc.a2005s+aseg.mgz will have a whole thalamus segmentation, but that is inherited from the aseg.mgz doug Kern, Mark wrote: > Hi Doug, > > Yes, the aparc.a2009s+aseg.mgz files were created and I have used them in a great deal of our analysis of large scale network connectivity of cerebral cortical regions. We have a desire to look at some subcortical structures that are part of the a2005s scheme but not included in the a2009s treatment, especially the subdivision of the thalamus. Any help in this matter would be greatly appreciated. > > Best Wishes, > Mark > > > On Mar 7, 2012, at 10:47 PM, Douglas Greve wrote: > > >> Hi Mark, was aparc.a2009s+aseg.mgz created? That is the new one. >> doug >> >> On 3/7/12 8:43 AM, Kern, Mark wrote: >> >>> Dear Freesurfer Mavens, >>> >>> After running "recon-all -all" on a set of anatomical data, I wished to used the aparc.a2005s+aseg.mgz in a connectivity analysis pipeline to create some ROI masks. I was particularly interested in the subcortical regions contained in the a2005s scheme. However, the aparc.a2005s+aseg.mgz file was not created during the recon-all processing run. Is there a way to get the a2005s segmentation data? >>> >>> Thanks for your help. >>> >>> Best, >>> >>> Mark >>> >>> Senior Research Scientist >>> Division of Gastroenterology and Hepatology >>> Departmernt of Medicine >>> Medical College of Wisconsin >>> Milwaukee, WI >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and properly >> dispose of the e-mail. >> >> > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable
by Ian Charest 08 Mar '12

08 Mar '12

Hi again More on this note: Using the previous stable version 4.3.0 that I have installed here, I have absolutely no problem in running the same process. ian From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ian Charest Sent: 07 March 2012 18:09 To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable Hi When running recon-all I get the following error: ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I called recon-all like so: recon-all -i /imaging/ic01/mridata/subject01/structurals/subject01.MR.SEQUENCE.0014.0001.2011.12.16.57.613319.8231038.IMA -all -subjid subject01 I checked the talairach_avi.log file (see the full report below), and the mistake happens at the call to mpr2mni305 MPR2MNI305_TARGET: Undefined variable. I searched the mailing list for similar errors and saw a similar post here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018445.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-May/018445.html> but in this user's case there seemed to be a problem with the MPRAGE image itself (the brain seemed "squashed") I checked the dimensions of my orig.mgz and they are ok (1x1x1). I had a look at my orig.mgz in tkmedit and all seems fine. Any Idea what could be going wrong? Best Wishes Ian Charest ====== talairach_avi.log: /imaging/ic01/subjects/subject01/mri /imaging/local/software/freesurfer/5.1.0/i686//bin/talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux l34 2.6.9-89.0.25.ELsmp #1 SMP Mon Apr 19 06:05:15 EDT 2010 i686 i686 i386 GNU/Linux Wed Mar 7 16:56:30 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mri_convert orig.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-1, 4.65661e-08, -4.09782e-08) j_ras = (-2.23517e-08, -3.72529e-09, -1) k_ras = (3.81842e-08, 1, -6.98492e-10) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 132.161; 0.000 -0.000 1.000 -103.886; -0.000 -1.000 -0.000 97.205; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Wed Mar 7 16:56:34 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ MPR2MNI305_TARGET: Undefined variable.

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recon-all exit with errors.
by Hellyer, Peter 08 Mar '12

08 Mar '12

Good Morning, List. I'm recon-all(ing) a bunch of T1 images using the command recon-all -i input.nii.gz -subject name -all -sd /path/to/subject/directory Most of the time, these are running just fine, but occasionally, they are exiting with error (recon-all.log attached). I don't understand what is going on, as the input data looks okay and I'm running the same command over and over (using PBS)…. Any help would be appreciated. Best Wishes Peter

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qdec
by Richter, Julia 08 Mar '12

08 Mar '12

Dear freesurfer experts, I am trying to run a volume analysis with qdec. One of my discrete variables has 3 three levels...Is Freesurfer capable of creating a FSGD file of a discrete variable like this? When I m running the analysis, the terminal also says "no contrasts specified" after trying to read the source surface. What is wrong here? Thank you all so much for your help, Julia

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FS 5.1 control points problem
by Tetiana Dadakova 08 Mar '12

08 Mar '12

Dear FS list, We started using FS 5.1 and encountered a problem with control points. After first recon-all some of the cortex (in occipital part) was missing, so we added control points and re-ran -autorecon2-cp -atorecon3. After that, the part of the brain with control points was removed from brainmask.mgz (Fig1). I never had this problem in 5.0, therefore I assume that something has been changed in 5.1 regarding cp. Could you please suggest what can be the problem and if it is described somewhere? Thank you, Tanja.

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Total WM and GM Vol in FS 5.0.0
by Dhinakaran Chinappen 08 Mar '12

08 Mar '12

Hi all, I am using Freesurfer 5.0.0, before the outputs for cortical and subcortical GM and WM were made available in the final output files. What is the best way to calculate total gray matter volume (cortical and subcortical)? Is it through mris_anatomical_stats or mri_segstats? Also, are there commands to calculate total cortical and total subcortical volumes of GM separately? As for total white matter, is using the sum of the volumes of Left-Cerebral-White-Matter and Right-Cerebral-White-Matter considered acceptable practice? Or should I go to the command line and use mris_wm_volume? Thanks in advance for the clarification, Dhinakaran.

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"Smart" concatenation in selxavg3-sess?
by Alex Kell 07 Mar '12

07 Mar '12

Hi Freesurfers, The selxavg3-sess's help and Freesurfer documentation say that selxavg3-sess creates a design matrix for each run, fits the glm for each run, and then combines the runs together to give summary data for the subject's whole session. Some of the fsfast 5 slides say it uses "smart" concatenation to combine each run's data -- what is "smart" concatenation? How does are the runs brought into alignment? Thanks! Alex Kanwisher Lab Manager McGovern Institute for Brain Research MIT

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aparc.a2005s+aseg.mgz
by Kern, Mark 07 Mar '12

07 Mar '12

Dear Freesurfer Mavens, After running "recon-all -all" on a set of anatomical data, I wished to used the aparc.a2005s+aseg.mgz in a connectivity analysis pipeline to create some ROI masks. I was particularly interested in the subcortical regions contained in the a2005s scheme. However, the aparc.a2005s+aseg.mgz file was not created during the recon-all processing run. Is there a way to get the a2005s segmentation data? Thanks for your help. Best, Mark Senior Research Scientist Division of Gastroenterology and Hepatology Departmernt of Medicine Medical College of Wisconsin Milwaukee, WI

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