Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

Failure to convert DICOM files
by Ed Gronenschild 27 Mar '12

27 Mar '12

Hi, I got an error during the first step in recon-all (Mac OS 10.6.8, FreeSurfer v5.1.0). The eror message in the log file is: WARNING: file ...../MR.1.3.12.2.1107.5.2.18.41016.201008031106017688438785.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header. This is strange because it is no mosaic file and all the files can be converted without any problems with e.g., dcm2nii and viewed with OSIRIX. Cheers, Ed

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Displaying FSL zstats onto FreeSurfer
by Zurcher Nicole 27 Mar '12

27 Mar '12

Hi everyone, I have two questions regarding FreeSurfer and FSL interoperation and it would be great if someone could help. 1) When displaying subject-level FSL FEAT data onto the FS volume using the command "tkmedit blobby orig.mgz lh.white -overlay ./featdir/stats/zstat1.nii.gz -overlay-reg featdir/reg/freesurfer/anat2exf.register.dat fthresh 1.3 -fmid 2.3 -fslope 1” (mentioned on http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html) What p-value does the threshold of 1.3 correspond to? Is it a zscore? 2) What would be the best way to display FSL group-level FEAT data (zstats) onto the FreeSurfer surface? As far as I understand, the FSL and FreeSurfer Interoperation website explains how to display subject level-feat on the surface. For the group-level data, it only explains how to run group-level analyses using mri_glmfit based on lower-level FSL FEAT directories. Is there a way to directly map the zstats from FSL group-level analyses onto the FreeSurfer surface? Thanks in advance for the help! Nicole

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amount of manual corrections in 5.1 related to aparc+aseg?
by Dorit Kliemann 27 Mar '12

27 Mar '12

Dear FreeSurfers, I'm working on a structural dataset and after running recon-all -all, I had to correct all cases (32 so far) from minimum pial/wm corrections to massive pial corrections (only three cases needed control points). Mostly, the corrections were needed due to remaining dura/skull. Initially, I tried to adjust the skull-stripping (either with changing the wsthresh or gcut for individual cases), however, those corrections were not always too successful (i.e. still remaining dura/skull), so I continued correcting manually. Are there any known/expected problems that could still arise with the aparc+aseg segmentations after (massive) corrections (i.e. all cases), even after redoing respective recon-steps with version 5.1? In the release notes, I only found that control points may adversely affect aseg... I checked the segmentations and so far I couldn't recognize any obvious/consistent flaws. I remember from working with version 4.1. that most cases need at least some corrections, but I don't have any experience with 5.1, yet. I'm specifically interested in the amygdala, but of course amygdala segmentations will be corrected manually. Thanks, Dorit Data were acquired on a 3T Tim Trio dataset (32 channel-coil, TR 1900ms, TE 2.52 ms, 1x1x1 voxel-size, TI 900ms, flip angle 9, ipad grappa2, bandwidth 170Hz/pixel, prescan-normalize). Data were initially processed with recon-all -all with version 5.1 on a linux cluster (scientific linux 6.1). Data were corrected and then re-run with respective recon-steps on a local Mac (OS 10.5.8) with freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.

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Re: [Freesurfer] Failure to convert DICOM files
by Ed Gronenschild 27 Mar '12

27 Mar '12

Hi Jamaan, Yes, I got the same error. Ed On 27 Mar 2012, at 13:36, Jamaan Alghamdi wrote: > Hi Ed, > > Have you tried using mri_convert command directly without running recon-all. > > Best wishes, > Jamaan > > Hi, > > I got an error during the first step in recon-all (Mac OS 10.6.8, > FreeSurfer v5.1.0). The eror message in the log file is: > > WARNING: file ...../MR.1.3.12.2.1107.5.2.18.41016.201008031106017688438785.dcm does not contain a Siemens ASCII header > has this file been anonymized? > ERROR: cannot unpack mosiacs without ASCII header. > > This is strange because it is no mosaic file and all the files can be converted > without any problems with e.g., dcm2nii and viewed with OSIRIX. > > Cheers, > Ed > > -- > Jamaan Alghamdi > 07779801950 > 0151 795 4627 > Magnetic Resonance & Image Analysis Research Centre (MARIARC) > University of Liverpool > Pembroke place > Liverpool > L69 3GE > > http://www.easyneuroimaging.com/ >

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-mprage flags
by Sabin Khadka 26 Mar '12

26 Mar '12

Hi all, What does -washu_mprage and -mprage flags do in autorecon step. How does it help in segmentation? -SK

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segmentation of the dural sinuses
by Jonathan A Winawer 26 Mar '12

26 Mar '12

Are there any tools associated with freesurfer to aid in segmentation of the dural sinuses (e.g., superior sagittal sinus, transverse sinus, straight sinus, etc) from a T1-weighted anatomical scan? Many thanks, Jon ******************************* Jonathan Winawer Stanford University Department of Psychology Jordan Hall, Building 01-420 450 Serra Mall Stanford, CA 94305 Phone: 650-725-1255 winawer(a)stanford.edu http://www-psych.stanford.edu/~winawer/

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Re: [Freesurfer] volume mapping
by Anastasia Yendiki 26 Mar '12

26 Mar '12

Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer. a.y On Mon, 26 Mar 2012, Johnson wrote: > Hi FS expert > I need to know the transformation matrix itself since I will do the > transformation in matlab. > I successfully transformed white matter fibers coordinates to T1 using AIR > 5.0 from LONI lab. > They provide a transformation matrix. > Now I want to transform the coordinates from T1 to Freesurfer space, so > my question is: what is the transformation matrix that relates the T1 > which FS have used for parcellation and segmentation with the aparc+aseg.mgz > file? > I searched the logs but couldn't find such matrix. > I don't want to do a registration step since it will be less accurate than > the one that was generated during the segmentation process. > Also is it just one transformation or a combination of transformations? > > thanks > >

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calculating DLPFC or frontal lobe grey and white matter volumes
by sam bedford 26 Mar '12

26 Mar '12

Dear All We want to find frontal lobe grey and white matter volumes in a patient group to compare it with control group. In particular, we want to see the grey and white matter volumes in the dorsolateral prefrontal cortex (DLPFC). However we seem to be having problems finding this region on the processed data for white matter volume (after recon-all command). It was previously suggested in this mailing list that we can get grey matter volume for the DLPFC by combining the following volumes: $hemi.G_frontal_middle.label $hemi.S_frontal_inferior.label $hemi.S_frontal_middle.label We are wondering how to get white matter volumes in the same region... If getting the DLPFC volume is difficult then can we just use the frontal grey and white matter volumes to make between group comparisons. From aseg and aparc files in the stats folder, adding all the following values below would give us frontal white and grey matter volumes. Or is there a simpler and less time consuming way to calculate grey and white matter volume in the frontal lobe? Frontal lobes - White Matter volume caudalmiddlefrontal lateralorbitofrontal medialorbitofrontal paracentral parsopercularis parsorbitalis parstriangularis precentral rostralmiddlefrontal superiorfrontal frontalpole Frontal lobes - Grey Matter volumes G_and_S_frontomargin G_and_S_paracentral G_and_S_subcentral QQQ??? G_and_S_transv_frontopol G_front_inf-Opercular G_front_inf-Orbital G_front_inf-Triangul G_front_middle G_front_sup G_precentral S_front_inf S_front_middle S_front_sup Thanks in advance Sam

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Talairach registration problem
by Gregor Strobbe 26 Mar '12

26 Mar '12

Dear All, Did someone already figured out a solution for this problem? I get exactly the same error every time I run recon_all There seems to be no answer on the mailing list yet Thank you Kind regards Gregor ---- Hi Avi, do you have any advise for Dana? thanks Bruce On Tue, 30 Jun 2009, Dana W. Moore wrote: Doug Yes, there is an error message in the talairach_avi.log--I am not sure what it means. The end of the log gives me this message: Dana imgrege: no voxels in register ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305/usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted At 06:34 PM 6/29/2009, Douglas N Greve wrote: The error msg asks you to look at transforms/talairach_avi.log. Have you and does it reveal anything? doug Dana W. Moore wrote: Hi all, I get the following error message during recon-all: ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305/usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Any idea why this is happening? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2...(a)med.cornell.edu _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2...(a)med.cornell.edu _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _________________

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normal vector projection
by Seok Lew 26 Mar '12

26 Mar '12

Hi, After freesurfer reconstruction, I tried to project surface normal vectors on the ribbon. I used the following scripts, but the projected vectors were out of the ribbon when I visualized it freeview. The vectors were placed outside of the ribbon. Anyone knows any idea ? fslregister --mov mri/orig.mgz --s xDS --reg rrr.dat --dof 12 --tmp ./tmp/ mri_surf2surf --s xDS --hemi lh --sval-nxyz pial --tval ./pl_100.mgz mri_surf2vol --surfval pl_100.mgz --hemi lh --surf pial --volreg rrr.dat --outvol pln_pribbon.mgz --fillribbon --template mri/orig.mgz Thank in advance, Seok Lew, Ph.D. MEG Core Laboratory Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School slew(a)nmr.mgh.harvard.edu

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Freesurfer March 2012