Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

bug in FS permutation
by Douglas N Greve 17 Jan '12

17 Jan '12

Hi Y'all, I have just found a bug in our implementation of the permutation test. It does not affect all permutations, so read on to figure out if it affects you. The bug is that the histogram that is created by the permutation simulation is always based on the last contrast in the analysis. The permutation p-value is computed from the histogram, so this means that the wrong histogram is being applied to the contrasts (except for the last contrast). This affects you IF: 1. You are doing permutation tests with mri_glmfit-sim or mri_glmfit to correct for multiple comparisons 2. You have more than one contrast 3. You are reporting p-values from a contrast that is not the last contrast on the mri_glmfit command-line 4. Note: the monte carlo simulations are not affected. Until I can find a better solution, the work-around is to run a separate instance of mri_glmfit for each contrast, then run mri_glmfit-sim separately for each mri_glmfit run. doug -- 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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Converting mgz to nii.gz
by Antonella Kis 17 Jan '12

17 Jan '12

Dear all, I am trying to convert my DTI image which was previous resampled to CVS space from an .mgz format to a .nii.gz format. When I resampled to CVS space I used the nearest interpolation. I used for converting this .mgz image to .nii.gz the mri_convert as you can see below: mri_convert --in_type mgz --out_type nii --out_orientation RAS /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz \ /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz I understood that --out orientation RAS states that I am flipping the image. Do I need to use this option? Even if I am using or not I see my image is having different direction than the .mgz image. Also while running with the option --out orientation RAS I saw that the program is doing a triliniar interp and I don't want to resample anymore my iamge just to converte this from mgz to nii. What is the best way I should do it? Thank you. Antonella

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Re: [Freesurfer] Converting mgz to nii.gz
by Lilla Zollei 17 Jan '12

17 Jan '12

Hi Antonella, If you are applying the morph to a mask file, then yes, the nearest neighbor interpolation shoudl be used. The masking option that you ask about below depends on whether you want to use wmparc to guide your masking (option 1) or whether you want to do the masking based upon intensity values found in the fa image (option 2). --Lilla On Tue, 17 Jan 2012, Antonella Kis wrote: > Dear Lilla, > > Many thanks for your reply and for your help. > > Regarding the way I resampled my fa data to the CVS space I was reading on the FSTutorial/Diffusion that if you wanted to resample a segmentation volume (such as wmparc or aseg) in CVS space, you would want to use the nearest neighbor (nearest) interpolation > option.The fa mask was calculated using the wmparc2diff as you can see below so I thought because I am using the wmparc which is a segmentation volume I should use for resampling the nearst interp. Please let me know if I am wrong. > > mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ > $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ > $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz > Is this the right way to calculate my fa-masked or I should use all my fa data only: > > mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ > $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz > Thank you very much! > Antonella > > ___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Monday, January 16, 2012 5:39 PM > Subject: Re: [Freesurfer] Converting mgz to nii.gz > > > Hi Antonella, > > You should be able to just do > > mri_convert /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz > > BTW, when resampling your FA data to CVS space, I think you should be using trilinear interpolation. We only suggest the nearest neigbour option for segmentation and parcellation files. > > --Lilla > > On Mon, 16 Jan 2012, Antonella Kis wrote: > > > Dear all, > > > > I am trying to convert my DTI image which was previous resampled to CVS space from an .mgz format to a .nii.gz format. When I resampled to CVS space I used the nearest interpolation. > > > > I used for converting this .mgz image to .nii.gz the mri_convert as you can see below: > > > > mri_convert --in_type mgz --out_type nii --out_orientation RAS /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz \ > > /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz > > > > I understood that --out orientation RAS states that I am flipping the image. Do I need to use this option? Even if I am using or not I see my image is having different direction than the .mgz image. Also while running with the option --out orientation RAS I saw > that > > the program is doing a triliniar interp and I don't want to resample anymore my iamge just to converte this from mgz to nii. > > > > What is the best way I should do it? > > > > Thank you. > > Antonella > > > > > > > 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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Newbie question: mean/stddev for volumes and thicknesses in an atlas
by Inati, Souheil (NIH/NIMH) [E] 17 Jan '12

17 Jan '12

Hi All, I have a very small set of patients and I would like to compare the volumes of subcortical structures and thickness across the cortex to those of a large normative set. I don't need all the underlying data, just means and standard deviations. Is such a set of measures available? Thanks, Souheil

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update version of tksurfer and freeview
by Knut J Bjuland 17 Jan '12

17 Jan '12

Hi When I was at the Freesurfer course in December we used an updated version if Tksurfer and Freeview. Is it possible to get a download link to thesse new version of Tksurfer and Freeview please? Cheers Knut J

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Postdoc position in neuroanatomical MRI of developmental dyslexia
by Irene.Altarelli＠ens.fr 17 Jan '12

17 Jan '12

Applications are invited for a postdoc position in the team of Franck Ramus, LSCP, Institut d'Etudes Cognitives, Ecole Normale Supérieure, Paris, France. The successful candidate will investigate neuroanatomical differences between dyslexic and control children, using high-quality 3T MRI images from diffusion and T1 sequences that have already been collected as part of an imaging and genetics project. The position is available from January 1st. Candidates should have a PhD and extensive research experience in cognitive neuroscience. Expertise with the analysis of neuroanatomical images will be a strong asset. Net salary will be a minimum of 2000â¬/month and will depend on the experience of the candidate. Further details and informal enquiries may be directed to Franck Ramus (franck.ramus(a)ens.fr) Applicants should send a letter of application, clearly outlining the candidate's expertise and research interests, along with a CV, and names of 2-3 references to franck.ramus(a)ens.fr, by February 1st. The position will remain open until a suitable candidate has been found.

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control points
by Alana Shepherd 16 Jan '12

16 Jan '12

Hello, I am running version 5.0, and am finding in a few cases that some areas (most commonly STG) are missing from the original brainmask - after adding control points and re-running the pipeline, these regions are still not being picked up in the surfs or in the aseg. Can you suggest any other way of remedying this? Many thanks Alana Shepherd

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problem applying morph with mri_vol2vol
by Gregory Kirk 16 Jan '12

16 Jan '12

Hi i am trying to transform/morph a tract created with tracula into my cvs template subject space, using v.5.0 i am thinking the bb register transformation i am using is not the correct one, but it seems the logical choice, but obviously not working good as forceps minor ends up wraped around the brain stem. here is what i run mri_vol2vol --targ /study5/aa-scratch/TEENEMO/freesurfer_subjects/033/mri/norm.mgz --m3z combined_to033_elreg_afteraseg-norm.m3z --noDefM3zPath --fsl /study5/aa-scratch/TEENEMO/freesurfer_local/toot/006//dmri/xfms/diff2anat.bbr.mat --mov /study5/aa-scratch/TEENEMO/freesurfer_local/toot/006/dpath/fminor_PP_avg33_mni_bbr/path.pd.nii.gz --out ./to033path.pd.nii.gz --interp trilin --no-save-reg thanks greg

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regenerating surfs after pial edits
by Tobia, Michael 16 Jan '12

16 Jan '12

Dear Freesurfer Experts, I am trying to create surfaces that can be used in afni/SUMA for cortical based inter-subject alignment. For most of my subjects your programs have worked perfectly. But I am having a problem for two subjects with dura residual from the skull stripping that is disotrting the pial surface and produces long protruding 'handles' stemming from the cortial surface once generated in SUMA. I have made edits to the offending voxels in the brainmask.mgz using tkmedit according to the tutorial, and subsequently re-run recon-all -autorecon2-pial -autorecon3 -subjid subj05, but the surfaces still appear as they were prior to the edits. I looked at the brain.finalsurfs and noticed that the red and yellow lines demarcating WM and pial surfaces where I had deleted offending voxels remain despite re-running recon-all, as if new surfaces had not been generated. Can you tell me what I am doing wrong? Is it possible to edit the offending surface markers themselves? Any help and advice woudl be greatly appreciated. ~michael Systems Neuroscience, NIN Universitatsklinikum Hamburg-Eppendorf -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus

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question about total gray matter volume.
by Mehul Sampat 14 Jan '12

14 Jan '12

Hi Folks, I saw that mri_segstats from v5.0 onwards has an option to measure the total gray matter volume (--totalgray). My question is, If I have dataset processed with FS v4.5, can I use the mri_segstats (from v5.0) to measure the total gray matter volume on this dataset ? Thanks Mehul

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