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30088 discussions

Please help: Registering to FSL feat- example_func2standard
by Michelle Umali 17 Apr '12

17 Apr '12

Hi Freesurfers, I ran reg-feat2anat to register freesurfer data to FSL feat in order to generate some binary masks. Afterwards I edited the FEAT registration to standard space via: reg-feat2anat --feat subjectX.feat --manxfm func2std and saved the registration. i want to use these example_func2standard edits, but I just now realized that I didn't add the -overwrite-exf2std flag. Is there anyway to generate a new example_func2standard.mat from the exf2std.register.dat that has the edits to replace the FSL-generated one? I would love to avoid re-editing everything. Many thanks for any help. Michelle

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subtracting segmented volumes
by Adil Javed 17 Apr '12

17 Apr '12

Hi, Is there a way to subtract segmented files in freesurfer? For example, aparc+aseg.mgz - aseg.mgz= aparc.mgz only? I am interested in looking only at the cortex. I find that label to volume conversion doesn't give me a nice segmented cortex, with some patchy areas of intensities lost. thanks, AJ

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reg-feat2anat --feat --manxfm func2std
by Michelle Umali 17 Apr '12

17 Apr '12

Hi Freesurfers, I ran reg-feat2anat and am now checking registration. For some subjects I had to edit the registration of feat to standard space. So, do I have to replace the example_func2standard.mat fsl's example_func2standard.mat in the reg folder or is this done automatically? Is this the only file that has to be copied over? Thanks. Michelle

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Longitudinal Edits, skull strip and wmcp, how to do this longitudinally
by Mark Fletcher 16 Apr '12

16 Apr '12

For some of my subjects, I need to make many different types of edits on my longitudinal data, but have a few questions regarding the order/how to do this. I have read the details of this website ( http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) but wanted to confirm a few things. In regards to the following questions, I have not yet run the "create base" yet for anything. Also, I am asking these questions because I already made all of the following edits (and others) on the cross-sectionals as described at ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) and need to know if this was the right time to do this, and what to do after? *For subjects that just need white matter control points:* For subjects that just need white matter control points, I have added them on each cross-sectional time point, and reprocessed them via the command (recon-all -autorecon2-cp -autorecon3 -subjid cp_before). Is the next step to simply run (recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all) pointing to the subjects that have been corrected with control points? Do I need to add any flags or additional commands for the base creation to take the white matter control points into account? Should I need to make any further edits to the "base" or longitudinals after this? *For subjects needing skull stripping and white matter control points*: A few of my subjects need both WMCP's and skull stripping adjustments? I'm assuming that you should do the skull stripping first and then the WMCP, is this correct? Does it matter? I am doing this to the cross sectionals only. * After reprocessing these, is the next step to simply run (recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all) pointing to the subjects that have been corrected with control points and skull strip? Do I need to add any flags or additional commands for the base creation to take the white matter control points into account? Should I need to make any further edits to the "base" or longitudinals after this?* *Does all this hold true if making manual edits of the skull* *Subjects that need Pial Edits amidst other things*: A few subjects need pial edits? I've done this to the crossectionals, is this appropriate (I couldn't tell from the longitudinal edits page? Any order that this should fit in? After reprocessing them for the edits, *is the next step to simply run (recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all) pointing to the subjects that have been corrected with the pial edits? Do I need to add any flags or additional commands for the base creation to take the white matter control points into account? Should I need to make any further edits to the "base" or longitudinals after this?* *Making Edits to White Matter:* One of my subjects seem to have lesions similar to those described here ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits) When/where do I edit this in the longitudinal processing stream? These subject also needs WMCP, is their an important order for doing these. *After reprocessing them for the edits, is the next step to simply run (recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all) pointing to the subjects that have been corrected to the white matter? Do I need to add any flags or additional commands for the base creation to take the white matter control points into account? Should I need to make any further edits to the "base" or longitudinals after this?* *Correcting Topological Defects:* When should I correct topological defects as described here ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect ). Same end questions as ones above about what to do after fixing these. *Filling Lateral Ventricle: *Another question about White matter edits. One of my subjects needs to have its lateral ventricle filled (aka, adding it to the white matter). When/where should I do this. After processing it, what commands to run to create base? Thanks for answering my many questions. I am very impressed at the functionality of FreeSurfer, but want to be sure I am using them correctly.

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Job offer for neuroscientist with focus on MR image analysis
by Prof. Dr. Michael Deppe 16 Apr '12

16 Apr '12

On behalf of the Medical Faculty of the University of Münster I forward the following offer for a postdoctoral position in Neuroimaging research: Kind regards, Michael Deppe ---------------------------------------------------------------------- Prof. Dr. rer. medic. Dipl.-Phys. Michael Deppe Universität Münster Klinik und Poliklinik für Neurologie Funktionelle Bildgebung Albert-Schweitzer-Campus 1, Gebäude A1 48129 Münster, Germany Tel. +49 (0)251-83-48174 FAX +49 (0)251-83-52064 deppe(a)uni-muenster.de ----------------------------------------------------------------------

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Re: [Freesurfer] mri_compute_volume_fractions
by Bruce Fischl 14 Apr '12

14 Apr '12

Hi Adrian this will create a voxel map with the % of each tissue class in each voxel. If you want the total %s, just read them out of the stats files and compute them directly. cheers Bruce On Sat, 14 Apr 2012, Adrian Garcia wrote: > Dear Bruce, > > thank you for the reply. So this function creates an image for wm/gm/csf. I was hoping for a table of values (i.e. percent of wm/gm/csf in the volume), is this possible or should I be looking at another function? > > Best wishes > Adrian > > >

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mri_compute_volume_fractions
by Adrian Garcia 14 Apr '12

14 Apr '12

I would like to have Freesurfer calculate the percentage of wm/gm/csf from an MRI volume (produced with mri_volsynth). I have run recon-all to completion and have a registration matrix from the MRI to the Freesurfer anatomical (tkregister2). It looks like mri_compute_volume_fractions will do what I want, but I am not sure what parameters to supply, particularly the <output stem>. Would somebody be able to point me to some documentation for this function or an example of the command line to output the segmentation information? Best wishes Adrian

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long.qdec.table.dat question
by Sabin Khadka 13 Apr '12

13 Apr '12

Hi all, I am trying to use qdec to perform comparison of cortical thickness in two different time periods. So I ran recon-all base and recon-all -long. then defined long.qdec.table.dat as fsid fsid-base years MRI_001_T1 MRI_001 0 MRI_001_T2 MRI_001 2 When I tried to run qdec it says it "cant find MRI_001_T1/surf/lh.thichkeness.fwhm10.fsaverage.mgh" which I think makes sense because I did not run qcache to smooth the surface. So my question is Is the way I am writing my lon.qdec.table.dat correct or should it be fsid fsid-base years MRI_001_T1.long.MRI_001 MRI_001 0 MRI_001_T2 .long.MRI_001 MRI_001 2 Also, if I need to run qcache should I run in MRI_001_T1 or MRI_001_T1.long.MRI_001. Thanks. Sabin

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created a new subcortical atlas; what's next?
by Anthony Dick 13 Apr '12

13 Apr '12

Hello, I successfully created a new subcortical atlas for the cerebellum (at least I think I did--not sure how to check it without running a new segmentation). If I want to apply this to many brains, I think I want to run: recon-all -subcortseg -subjid <subject name> How do I tell it to call, e.g., RB_all_withskull_2012-04-13.gca instead of e.g., RB_all_withskull_2008-03-26.gca. Basically, I want to apply the new cerebellar parcellation to existing freesurfed brains. Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://www.fiu.edu/~adick Lab Webpage: http://dcn.fiu.edu

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bbregister for fmri FEAT data
by Erlend Hodneland 13 Apr '12

13 Apr '12

Hi, we are trying to register fmri FEAT data (example_func.nii) to the anatomical scan (processed in Freesurfer) using bbregister to opt. the affine registration before running FNIRT. However, the orientation of the registered image is flipped around and is incorrect after applying bbregister. We have tried: 1) bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-header --bold --o example_func2highres-fs.nii 2) bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-fsl --bold --o example_func2highres-fs.nii 3) bbregister --s subj_501 --o example_func2highres-fs.nii --feat "myfeatdirectory" 4) tkregister2 --mov example_func.nii --regheader --reg tkreg.dat (this one looks correct) followed by bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-reg tkreg.dat --bold --o example_func2highres-fs.nii 5) reorienting to match the highres: fslorient -swaporient example_func fslswapdim example_func x -y z example_func_swap (correct orientation) followed by bbregister --s subj_501 --mov example_func_swap.nii.gz --reg register.dat --init-fsl --bold --o example_func_swap2highres-fs.nii with the output being flipped in wrong orientation for all options. We would greatly appreciate if you have any suggestions for how to overcome this problem! Cheers/Sincerly/All best Erlend Hodneland

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