Freesurfer February 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
199 discussions

Question regarding sig.mgh
by Antonella Kis 24 Feb '12

24 Feb '12

Dear All, 1)I would like to know what is the best way in catching the uncorrected clusters results from the sig.mgh for a structural study: Should I use the: mri_glmfit-sim \ --glmdir lh.GroupAnalysis_Thickness_15.glmdir \ --cache 2 pos \ --cwpvalthresh .99 \ --overwrite But in this case I am not getting all the clusters regarding their significance after correction by multiple comparison? I don't want the clusters from multiple comparisons just the uncorrected one. I am not sure why when I look to my clusters in QDEC I get a different p value for the uncorrected results sig.mgh that the one cached with the --cwpvalthresh .999 for example from QDEC for one cluster rostralmiddlefrontal in sig.mgh I got p =0.00338 while with the catche option and --cwpvalthresh .999 I got cwp 0.75890. I am doing something wrong? 2) If I know the MNI coordinates how I can get the location I mean the segmentation or annotation location of my clusters to the nears cortical label? Many thanks. AK

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fsaverage error - too many levels of symbolic links
by Gibbard, Clare 24 Feb '12

24 Feb '12

Hi, I am running recon-all on several scans, but it is exiting with an error. I think the error is occurring because my symbolic link to fsaverage is self-referential. However, the symbolic link is generated automatically during recon-all so I cannot see how to correct it. I have tried deleting the fsaverage from my subjects directory and re-running recon-all, but this did not work. I can see that others have had this error before, but I can't see the solution. Are you able to help? I have previously run recon-all without getting this error. Thank you. ls -l /home/clare/freesurfer/freesurfer/subjects/fsaverage gives this: lrwxrwxrwx 1 clare clare 52 2012-02-17 08:27 /home/clare/freesurfer/freesurfer/subjects/fsaverage -> /home/clare/freesurfer/freesurfer/subjects/fsaverage Here is the error: #@# BA Labels lh Fri Feb 17 08:27:35 GMT 2012 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /home/clare/freesurfer/freesurfer/subjects; ln -s /home/clare/freesurfer/freesurfer/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject subject_001 --trglabel ./lh.BA1.label --hemi lh --regmethod surface Too many levels of symbolic links mri_label2label: could not open label file /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label srclabel = /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = subject_001 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/clare/freesurfer/freesurfer/subjects FREESURFER_HOME /home/clare/freesurfer/freesurfer Loading source label. Invalid argument ERROR reading /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux clare-OptiPlex-990 2.6.35-32-generic #64-Ubuntu SMP Tue Jan 3 00:47:07 UTC 2012 x86_64 GNU/Linux recon-all -s subject_001 exited with ERRORS at Fri Feb 17 08:27:35 GMT 2012 Best wishes, Clare

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Problem with preproc-sess per-session and question about registration
by Wiegand, Katrin 24 Feb '12

24 Feb '12

Hi, I have two short questions concerning motion correction using preproc-sess and registration files 1) Running preproc-sess using per-session as e.g. like this preproc-sess -per-session -fwhm 0 -sliceorder siemens -surface vpID lhrh -s vpID -fsd bold -mni305 should result in a "fmc" output stem, doesn't it? This however, this is not the the case (I received "fmcpr"), so I'm wondering whether the error occured (only) at the labeling stage or whether motion correction was indeed computed for each run separately (I also received register files for each run, i.e. in each bold/run directory, rather than "global ones" within the bold directory). Is this a known issue? 2) Furthermore I'd be very glad if someone could shed some light on the registration process (using fslregister-sess) for -per-run mc and the various register-files that are produced. In particular, I do not understand how the output of the statistical analysis of the functional data (averaged over all runs) is mapped onto the high resolution anatomical data, when every run is registered seperately. Which register file is needed in order the visualize the results? And what about checking the accuracy of the registration, do I have to check this for every run? I am using freesurfer Version 5.1.0 (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0) on ubuntu 11.10 (64b). Thanks a lot in advance, Katrin

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white matter edits
by cloud.ctrl＠me.com 23 Feb '12

23 Feb '12

According to the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits, we should be looking for these holes in the white surface, but when I looked at my processed data using tkmedit SUBJECT brainmask.mgz -aux wm.mgz -surfs, I saw many such holes. They seem to be ubiquitous throughout all 20 of the brains I have processed. Some might be true mistakes in the white matter surface, but I thought maybe some might just be holes that appear because of the shape of sulci moving through 3D space. Or perhaps my Talairach is off? Is there any material that instructs how to tell the difference between holes which need to be fixed and those that don't? Thank you, Vincent

2 1

Fixing talairach registration
by cloud.ctrl＠me.com 23 Feb '12

23 Feb '12

After reading the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach, I understand that I should be using "tkregister2 --mgz --s SUBJECT --fstal --surf orig" when editing my talairach transform. I have been somewhat successful at this, but I was wondering if there might be another way to adjust talairach registration, perhaps by specifying anterior/posterior commissure alignment, etc?

2 1

SupraTentorial calculation
by Michael Harms 23 Feb '12

23 Feb '12

Hi Doug or Nick, I was wondering if you could clarify once exactly how the SupraTentorial volume in the aseg.stats is calculated from an algorithmic perspective. In particular, it isn't simply the sum of CortexVol + CorticalWhiteMatterVol + SubCortGrayVol, as implied by the Wiki. thanks! -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

2 3

Contrasts
by Allie Rosen 23 Feb '12

23 Feb '12

Hi, I am trying to figure out the contrasts to use for a study. I am comparing age matched patients and controls (all female). The FSGD file has 4 columns, but I'm not sure how to make an appropriate contrast matrix. Any guidance would be appreciated. I can't seem to find an applicable example on the wiki. Thanks, Allison

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overlay problem
by LAOUCHEDI MAKHLOUF 23 Feb '12

23 Feb '12

hi all i have still a problem to load an activation map on a pial surface (colin27). here are the steps followed to this end : first i run bbregister : bbregister --s colin27 --mov /home/mlaouche/bashr/V8.nii.gz --init-fsl --reg /home/mlaouche/bashr/regester1.dat --bold --surf pial then i used tksurfer to see the result which seems good: tkregister2 --mov /home/mlaouche/bashr/V8.nii.gz --reg /home/mlaouche/bashr/regester1.dat --surf i used mri_vol2surf this way : mri_vol2surf --src /home/mlaouche/bashr/V8.nii.gz --out /home/mlaouche/makh_free/v80.mgz --srcreg /home/mlaouche/bashr/regester1.dat --hemi lh i used again tksurfer to load first colin27 : tksurfer -colin27 lh pial then file/load overlay to load v80.mgz no overlay was mapped

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total gray matter volume
by Yolanda Vives 23 Feb '12

23 Feb '12

Dear Freesurfer experts, In Freesurfer v5.1, aseg.stats files give the value of total gray matter volume. Is this label in the annotation file? How can I know which voxels from the brain are considered as gray matter? Thank you in advance, Yolanda

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Re: [Freesurfer] Freesurfer and MATLAB
by Martijn Steenwijk 23 Feb '12

23 Feb '12

?h.aparc.stats gives an average in the different labels. You could also export the labels, then it should give - on average - the same results. Best, Martijn On Wed, Feb 22, 2012 at 9:51 PM, Antonella Kis <atorok9(a)yahoo.com> wrote: > Dear Marijn, > > Thanks again for your help. I tried to do the conversion but I am not sure > if I chooses the right files because I am not getting the same values like > the one from my lh.aparc.stats stats file. I need to get as output the > NumVert and ThickAvg as a table or ascii file. > > Thank you for helping again. > Antonella > > ------------------------------ > *From:* Martijn Steenwijk <martijnsteenwijk(a)gmail.com> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Sent:* Wednesday, February 22, 2012 2:34 PM > > *Subject:* Re: [Freesurfer] Freesurfer and MATLAB > > For the number of vertices, you could use mris_convert and convert the > surface files (overlapped with thicknesses) to ascii. > > Best, > Martijn > > On Wed, Feb 22, 2012 at 8:16 PM, Antonella Kis <atorok9(a)yahoo.com> wrote: > > Hi Martijn, > > Thank you very much for your prompt response. I knew about this option but > it doesn't let me get the no. of vertices just the thickenss which I want > but I need the no. of vertices too. Can you please help? > > MAny thanks. > AK > > ------------------------------ > *From:* Martijn Steenwijk <martijnsteenwijk(a)gmail.com> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, February 22, 2012 1:11 PM > *Subject:* Re: [Freesurfer] Freesurfer and MATLAB > > You could store them as a table (aparcstats2table), you can open the > resulting text file with matlab. > > Best, > Martijn > > > On Wed, Feb 22, 2012 at 6:59 PM, Antonella Kis <atorok9(a)yahoo.com> wrote: > > Dear All, > > > Is there a way that I can open my rh.aparc.stats files (saved in stats > after recon-all) in MATLAB as a matrix? I would like to concatenate all the > rh.aparc.stats files from all my subjects. > > Many thanks, > Antonella > > _______________________________________________ > 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. > > > > > > > >

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Freesurfer February 2012