Freesurfer

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Re: [Freesurfer] pet partial volume correction
by Douglas N Greve 30 Jun '11

30 Jun '11

Actually, I think it only will affect the volume measurement for each structure, so that's no good. There is not a flag to mri_segstats that will do this. If you have a registration between your native pet data and the FS anat, then you can use mri_compute_volume_fractions regfile.dat pet.nii pvf This will create pvf.{gm,wm,csf}.mgz You can then correct the pet with something like fscalc pet.nii div pvf.gm.mgz pet.pvf.nii You can map the aparc+aseg into the pet space using mri_label2vol (and the reg from above), then use mri_segstats with the files in the native pet space. doug corinna bauer wrote: > Hi Doug, > I will give that a try. How will this account for the p.v. in pet > data? Does it remove the voxels that are mixed tissue classes? Does it > account for partial volume effects between neighbouring grey matter > structures? > Corinna > > On Wed, Jun 8, 2011 at 1:06 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Corinna, > try adding --pv mri/norm.mgz > doug > > corinna bauer wrote: > > Hi all, > I am wondering if partial volume is taken into account when > calculating average uptake values of pet data. I know that > aseg.stats takes partial volume into account and I am > wondering if there is something similar in place for pet data? > From what I gather, most people when using FreeSurfer correct > for partial volume effects by regressing out cortical > thickness, but no basis for this correction method has been > provided. Any insight would be appreciated. > > n.b. to obtain the pet uptake values I used mri_segstats --seg > mri/aparc+aseg.mgz --sum pet.segstats.dat --i $petanat --ctab > rois.txt > > Thank you, > Corinna > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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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Missing white matter
by Knut J Bjuland 30 Jun '11

30 Jun '11

Hi I have mri picture where there is a large area where white matter is marked as grey. I might also add that this patient has enlarged ventricle and less white matter. I can not send the files on the list, I can however send the files if I get an addresses to send them too. What I ca I say howevere is that in this particulare areas are there none white matter from the cortex to the collusum. Cheers Knut J

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long_mris_slopes
by Seán Froudist Walsh 30 Jun '11

30 Jun '11

Dear FreeSurfers, I am looking for a little help comparing longitudinal data. I have three timepoints on each patient and have been able to get individual spc-thickness maps using the long_mris_slopes command where my table included all three time points. I would however like to compare different timepoints with each other: tp3-tp2 and tp2-tp1. I was hoping it would be as simple as specifying a new qdec table including (for example) only tp3 and tp2, and giving new output names using the following command long_mris_slopes --qdec ./qdec/long.qdec.tableTP23.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --out-avg=long23.thickness-avg.mgh --out-rate=long23.thickness-rate.mgh --out-pc1=long23.thickness-pc1.mgh --out-spc=long23.thickness-spc.mgh --out-stack=long23.thickness-stack.mgh --out-label=long23.cortex --time scan --qcache fsaverage but I get the following error: mris_calc: Sorry, but I seem to have encountered an error. While making backup of internal data arrays, it seems that some of the backups already exist. I'm not really sure what the internal data arrays are, and would greatly appreciate any help. Many thanks in advance and all the best, Seán

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Cortical Thickness
by leonardo kay 30 Jun '11

30 Jun '11

Hi Freesurfer experts. Do anyone know how to measure the cortical thickness of an specific brain area? I have been using mris_anatomical_stats but it only outputs the brain cortical thickness of the requested hemisphere. Best regards. -- Leo Kay.

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Over-smoothing of pial surface
by Yagna Pathak 29 Jun '11

29 Jun '11

Hi, I am trying to extract the pial surface for one of my subjects using freesurfer. Unfortunately, the last couple times that I ran recon-all, it generated a surface that was overly smoothed. I suspect this is due to a poor contrast in my MRI images. I tried to edit them via matlab and run them again. First, I got a talairach transform error and when I re-ran it with the -notal-check flag, I got a global region empty error. I was wondering if there is a way to enhance the mri images in freesurfer to obtain better contrast for a more accurate pial surface. Please let me know what is the best way to tackle this problem. I do not think it's the version of freesurfer, because the pial surface was created fine for some of the other subjects. Thank you, YP

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SupraTentorial Volume question
by Righart, Ruthger Dr. 29 Jun '11

29 Jun '11

Dear Freesurfer experts, I posted one week ago a question about the SupraTentorial Volume that is indicated in the aseg.stats but unfortunately did not receive any suggestions as yet. 1. SupraTentorial Vol. is defined as Cortex + CorticalWhiteMatter + SubCortGray (http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats) but when I sum up these columns myself from the aseg.stats I do not arrive at the exact value of SupraTentorial Vol that is indicated in the same aseg.stats. For some of my subjects this value is higher, for some it is lower. What could be the reason for these differences? Is CSF and ventricle volume already subtracted from the SupraTentorial Volume? 2. Is it possible to exclude lesions from the volume-based measures by incorporating a self-defined lesion mask for each subject? Any help or suggestions is very much appreciated! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany ruthger.righart(a)med.uni-muenchen.de

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error using recon-all function
by Ryan Hutten 29 Jun '11

29 Jun '11

Hi, I am currently trying to use the recon-all function. It works fine on an older computer, but my group is attempting to get freesurfer up and running on a newer computer. The subject data is located in a folder called 2645166 as shown in the following command. When I run the command: recon-all -s 2645166 -all I get the following error after the script runs for about a minute: ERROR: avi2talxfm failed, see transforms/talairach_avi.log Linux dell3 2.6.35.6-45.fc14.x86_64 #1 SMP Mon Oct 18 23:57:44 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux The output of your bugr script gives: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: Fedora release 14 (Laughlin) Kernel info: Linux 2.6.35.6-45.fc14.x86_64 x86_64 A brief internet search found nothing regarding this avi2talxfm function. Any suggestions and/or help would be greatly appreciated. Thanks,

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Re: [Freesurfer] Freesurfer Digest, Vol 88, Issue 86
by Antonella Kis 29 Jun '11

29 Jun '11

Good afternoon Bruce, I am not sure what video card I am using (and I am not sure how to do the updating for my video driver) but I could see these surfaces on the same computer while using an old Freesurfer version V.5.0. I saved this old version on my computer under freesurfer_backup and I re-installed the new version V.5.1.0. (my FREESURFER_HOME directory is directed to the new version v.5.1.0). I wonder if this maybe the reason or there maybe some problem with my insatllation? Many thanks for helping. Antonella ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: Wednesday, June 29, 2011 12:00 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 88, Issue 86 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Error with Tkmedit (Bruce Fischl) ---------------------------------------------------------------------- Message: 1 Date: Wed, 29 Jun 2011 10:49:56 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error with Tkmedit To: Antonella Kis <atorok9(a)yahoo.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <alpine.LRH.2.00.1106291049290.8015(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-15" Hi Antonella what video card are you using? Did you try updating your video driver? cheers Bruce On Wed, 29 Jun 2011, Antonella Kis wrote: > > Good morning, > > Thank you very much Bruce. I attached the tiff file and I am posting my message again on the list: > > I am having problem with tksurfer. > > When I run: > > ?tksurfer lh inflated > > for NPI002, the image is looking totally weird. I don't understand why I cannot get the correct lh inflated since there is no error while running tksurfer. > > ?I attached the tiff? image for the lh inflated for the NPI002 case after running tksurfer. I get similar image for the bert's data included as a freesurfer sample data. > > > Thank you! > Antonella > > > ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 88, Issue 86 ****************************************** 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. ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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Re: [Freesurfer] Error with Tkmedit
by Bruce Fischl 29 Jun '11

29 Jun '11

Hi Antonella what video card are you using? Did you try updating your video driver? cheers Bruce On Wed, 29 Jun 2011, Antonella Kis wrote: > > Good morning, > > Thank you very much Bruce. I attached the tiff file and I am posting my message again on the list: > > I am having problem with tksurfer. > > When I run: > > tksurfer lh inflated > > for NPI002, the image is looking totally weird. I don't understand why I cannot get the correct lh inflated since there is no error while running tksurfer. > > I attached the tiff image for the lh inflated for the NPI002 case after running tksurfer. I get similar image for the bert's data included as a freesurfer sample data. > > > Thank you! > Antonella > > >

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registration with Melodic
by Kat Mott 29 Jun '11

29 Jun '11

Hi all, I have manually registered fMRI data that I want to run ICA on, and I want Melodic to use my register.dat file, not re-register the data using its own algorithm. Since there doesn't seem to be any way to use the register.dat file as an input, I've been trying to figure out a way to apply the registration info to the .nii file and then simply uncheck the registration options in Melodic. I used a bit of code I found in the forum archives to try this, which created, using the f.nii and register.dat file, a file called f.anat.nii. But when I tried to use this as the 4D input for Melodic I got the error 'Child process exited abnormally.' I used the following to perform the transformation into f.anat.nii: mri_vol2vol --mov f.nii --reg register.dat --fstarg --o f.anat.nii Any thoughts on how to create an input that Melodic will accept so that it will use my registration? Thanks much, Kat

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