Freesurfer July 2012

freesurfer@nmr.mgh.harvard.edu

128 participants
194 discussions

Thickness and variable plot in glmfit
by Jeni Chen 30 Jul '12

30 Jul '12

Hello again, In Qdec we get a plot of the data for a particular vertex showing the variable and the thickness in the x, y axis respectively. Is there a way to get the same plot when using glmfit? Where do I find the data for the plot? Thank you! Jeni Chen

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Re: [Freesurfer] Smoothing in -qcache and the -fwhm option in mri_glmfit
by Douglas N Greve 30 Jul '12

30 Jul '12

Hi Jeni, you should not smooth with both. If you want to smooth within a given label with surf2surf, pass that label to surf2surf then don't smooth with glmfit. doug On 07/30/2012 12:46 AM, Jeni Chen wrote: > Hi Doug, > > When you say "If you smooth using surf2surf, then do not smooth using > glmfit..." are you referring to smoothing the whole hemisphere, or > with a label? In other words, if I had asked surf2surf to smooth only > inside a label, then no need to smooth again in glmfit. But if I did a > smoothing of 10mm in surf2surf on the entire hemisphere instead (i.e. > without "--label" option in surf2surf), then I will need to do > smoothing in glmfit. Did I get it right? > > By the way, thank you for replying- on midnight Sunday! (unless you > are in a different time zone...) > > Jeni > > > On 2012-07-30, at 12:04 AM, Douglas Greve wrote: > >> Hi Jeni, usually you smooth with surf2surf and include a mask or >> label to indicate that it should only be smoothed inside the >> mask/label. mri_glmfit will create a mask from non-zero voxels; if >> you ask glmfit to smooth, then it will only smooth inside of the >> mask. If you smooth using surf2surf, then do not smooth using glmfit. >> doug >> >> >> >> >> >> On 7/29/12 11:49 PM, Jeni Chen wrote: >>> Now I'm confused... So if I included a mask in my GLM analysis >>> (which I did), then I should add the -fwhm option in mri_glmfit? If >>> that's the case, does that mean my -y input file should be >>> unsmoothed to avoid double-smoothing? >>> >>> Jeni >>> >>> >>> On 2012-07-29, at 11:31 PM, Douglas Greve wrote: >>> >>>> Mostly yes. The one in mri_glmfit will also do smoothing within a >>>> given mask by default, but basically they do the same thing. >>>> doug >>>> >>>> On 7/29/12 11:15 PM, Jeni Chen wrote: >>>>> So essentially the -fwhm option in mri_glmfit does the same thing >>>>> as mri_surf2surf --fwhm ? Just want to make sure... Thanks again! >>>>> >>>>> Jeni >>>>> >>>>> >>>>> >>>> >>>> >>>> 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] tcsh: tailarach_avi: Command not found
by Fidel Vila 30 Jul '12

30 Jul '12

Hi Doug. The missing files are NOT in $FREESURFER_HOME/bin; So, I guess that's why they are not found even though the path is set up in the system PATH variable. Suggestions? Fidel Are the missing files in $FREESURFER_HOME/bin and is that path in your system PATH variable? On 07/26/2012 01:29 PM, Fidel Vila wrote: > Thanks for your prompt reply, Doug. > > I've been checking and following the wiki instructions with regards to > setting up proper paths, and I could not find an obvious (to me) > problem there. > > I attach a file with things I have tried and issues I have found. > > Further advice will be greatly appreciate it. > > Many thanks, > > Fidel > > > > > > On 25-Jul-12, at 8:22 PM, Douglas Greve wrote: > >> did you set up your environment so that your path environment >> variable has all the proper paths in it? Look at the wiki for >> instructions. >> doug >> >> On 7/25/12 7:57 PM, Fidel Vila wrote: >>> Hi Freesurfer experts, >>> >>> I recently installed FS (PowerPC architecture version available on >>> FS website) on a Mac OS X 10.4.11 and I get the attached output >>> error when running recon-all. >>> >>> Advice on how to troubleshoot this would be appreciate. >>> >>> Thanks, >>> >>> Fidel >>> >>> >>> >>> _______________________________________________ >>> 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. >> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Fidel Vila-Rodriguez, MD, FRCPC Clinical Assistant Professor, Faculty of Medicine, Dpt. of Psychiatry, University of British Columbia UBC Clinician Investigator Fellow UBC Graduate Program in Neuroscience Ph.D Candidate BC Mental Health and Addiction Research Institute A3-128-4, 938 West 28th Ave Vancouver, BC V5Z 4H4 Tel: 604-875-2000 Ext. 4732 Fax: 604-875-3871

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Re: [Freesurfer] Smoothing in -qcache and the -fwhm option in mri_glmfit
by Douglas Greve 30 Jul '12

30 Jul '12

Hi Jeni, usually you smooth with surf2surf and include a mask or label to indicate that it should only be smoothed inside the mask/label. mri_glmfit will create a mask from non-zero voxels; if you ask glmfit to smooth, then it will only smooth inside of the mask. If you smooth using surf2surf, then do not smooth using glmfit. doug On 7/29/12 11:49 PM, Jeni Chen wrote: > Now I'm confused... So if I included a mask in my GLM analysis (which > I did), then I should add the -fwhm option in mri_glmfit? If that's > the case, does that mean my -y input file should be unsmoothed to > avoid double-smoothing? > > Jeni > > > On 2012-07-29, at 11:31 PM, Douglas Greve wrote: > >> Mostly yes. The one in mri_glmfit will also do smoothing within a >> given mask by default, but basically they do the same thing. >> doug >> >> On 7/29/12 11:15 PM, Jeni Chen wrote: >>> So essentially the -fwhm option in mri_glmfit does the same thing >>> as mri_surf2surf --fwhm ? Just want to make sure... Thanks again! >>> >>> Jeni >>> >>> >>> >> >> >> 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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Re: [Freesurfer] Smoothing in -qcache and the -fwhm option in mri_glmfit
by Jeni Chen 29 Jul '12

29 Jul '12

So essentially the -fwhm option in mri_glmfit does the same thing as mri_surf2surf --fwhm ? Just want to make sure... Thanks again! Jeni

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converting to mgz error
by Skyler Gabriel Shollenbarger 29 Jul '12

29 Jul '12

Hi, Trying to convert a file to mgz and keep getting a 'document file' instead of the freesurfer mgz file. This is the command I used: mri_convert -ot mgz XXXXXXXX-anat+orig.BRIK freesurfer/mri/orig/001.mgz Any suggestions? Thanks! Skyler -- Skyler G. Shollenbarger Graduate Student - UWM Brain Lab Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee

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Smoothing in -qcache and the -fwhm option in mri_glmfit
by Jeni Chen 29 Jul '12

29 Jul '12

Hello Freesurfer experts, Just a question about smoothing. I did recon-all -qcache to get pre-smoothed fsaverage surface at 0, 5, 10, 15, 20 and 25mm FWHM, so for mris_preproc I used the "--cache-in" option (eg. for the *10mm.fsaverage file). When I run mri_glmfit, I see the option "--fwhm". Is this option for those who did not pre-smooth their data so that they can do the smoothing there? If I'm using a *.thickness.10.mgh file (10mm FWHM) obtained from the previously described steps as my input file (--y), then by specifing again a value in --fwhm does it mean I'm 'double' smoothing my data? Jeni ------- Jeni Chen, M.Sc. Agente de recherche Laboratoire de recherche en neuropsychologie de la douleur Pav. Paul-G. Desmarais, Université de Montréal CP 6128, Succ. A, Montréal, QC H3C 3J7 Tel: 514-343-6111 x4359

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pial edit question
by Cat Chong 28 Jul '12

28 Jul '12

Dear Experts, I am occasionally noticing some 'pinching' on the inflated brain surfaces around the temporal lobe pole. When I check the brainmask.mgz files, the raised areas are due to a 'bubble' of pial surface forming on top of pial surface. Upon checking white matter and grey matter boundaries, the pial surface should really not be separated as a "bubble", but should in fact be all one surface. What would you suggest would be the best way to fix this? The white matter seems to be fine. Best Regards, Catherine

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recon-all error
by Soo-Eun Chang 27 Jul '12

27 Jul '12

Hello, I've encountered an error message on a couple of my subjects while trying to preprocess for/run qdec. Here is my info copied from running bugr: FREESURFER_HOME: /export/data1/tools/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: Red Hat Enterprise Linux Workstation release 6.3 (Santiago) Kernel info: Linux 2.6.32-131.4.1.el6.x86_64 x86_64 Additional Info: 1) Subject name: NF108_11 (SUBJECTS_DIR: /export/data2/PI/freesurfer_subjects) 2) the entire command-line executed: recon-all -s NF108_11 -qcache 3) the error message generated: please see attached recon-all.log, recon-all.error One thing to note is that this subject's original recon-all -all was done using a previous version of FS while the recon-all -qcache command was run after a version update. I'm not sure if this messed things up, but thought I'd mention it. Thanks in advance for your help! Soo-Eun

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Converting labels to individual volumetric masks
by Antonella Kis 27 Jul '12

27 Jul '12

Dear All, I want to use cingulate bundle as ROIs more exactly mask for fiber tracking. Can I use different aseg than the one from Freesurfer for examples can I use segmentation from JHU-WhiteMatter-labels-1mm.nii.gz and their labels JHU-WhiteMatter-labels-1mm.txt to get a mask of my cingulate bundle in my diffusion space for each individual subject. Is the following correct: 1) mri_convert -rl [path to subject]/DATA/s001/nodif.nii.gz -rt nearest JHU-WhiteMatter-labels-1mm.nii.gz s001_aseg2dif.nii.gz 2) fslmaths /[path to subject]/DATA/s001_aseg2dif.nii.gz -uthr 35 -thr 35 /[path to working directory]/ROIS/Cingulum_(cingulate_gyrus)_R.nii.gz 3) fslmaths Cingulum_(cingulate_gyrus)_R.nii.gz –div 35 Cingulum_(cingulate_gyrus)_R.nii.gz If I want to run for the cingulate bundle the tractography should I repeat this steps for: 36 Cingulum_(cingulate_gyrus)_L 37 Cingulum_(hippocampus)_R 38 Cingulum_(hippocampus)_L Thank you for your help. Antonella

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Freesurfer July 2012