Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Regarding turning of labelling of hypointensities and choroid plexus
by Kathrine Skak Madsen 21 May '09

21 May '09

Hi FreeSurfer Experts Is there a way to turn of the labelling of hypointensities and choroid plexus? Thank you in advance. Best wishes Kathrine

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flipping freesurfer format brain (mirror image)
by xforever＠ucla.edu 21 May '09

21 May '09

Hi everyone, my name's Andy, I am a researcher in UCLA brain mapping group using Freesurfer we successfully generated the Surface or the vervet monkey brain, and our next step is to perform a surface segmentation using an .gcs file we created by hand. If there's anyway to flip the freesurfer format surface like .pial, .white, we'd only need one .gcs file for both hemisphere and that'd save us a lot of time. I tried using mris_transform with a xfm file, but the results turned out very weird. thanks in advance for the help Andy

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how to get fsaverage after recon-all
by karlkarl 21 May '09

21 May '09

Hello, I have finished the recon-all on all the participants and ready for the group analysis. But I didn't find the fsaverage. Did I miss someting in the recon-all? How can I get the fsaverage (If I have two groups, do I need fsaverage for each group)? thanks a lot! Karl _________________________________________________________________ Messenger安全保护中心，免费修复系统漏洞，保护Messenger安全！ http://im.live.cn/safe/

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Error unpacking dti scans
by Jesse Friedman 21 May '09

21 May '09

I've noticed that an error is consistently reported in the unpack log file when I unpack dti scans for any subject: INFO: this run has an error, but trying anyway For example, if I try to unpack the dti scan for subject RMCON032, whose data is in /space/archive/216/siemens/TrioTim-35006-20090508-140454-440000, the dcmdir-info output is: PatientName RMCON032 StudyDate 20090508 StudyTime 140454.440000 <snip> 000024 ep_b0#1 DIFFUSION_HighRes 440000-000024-000001.dcm 000025 ep_b0_700 DIFFUSION_HighRes 440000-000025-000001.dcm 000026 ep_b700t DIFFUSION_HighRes 440000-000026-000001.dcm 000027 ep_b0_700 DIFFUSION_HighRes 440000-000027-000001.dcm 000028 ep_b700 DIFFUSION_HighRes 440000-000028-000001.dcm 000029 ep_b0_700 DIFFUSION_HighRes 440000-000029-000001.dcm 000030 DIFFUSION_HighRes 440000-000030-000001.dcm <snip> And I enter the command: unpacksdcmdir -src . -targ $SUBJECTS_DIR/RMCON032 -run 24 dti_test nii f.nii -fsfast -log dti_test.log The unpack.log file contained the warnings and errors below (Also: I expected the log filed to be named dti_test.log so it wouldn't overwrite the unpack.log file I already had for the subject, but instead it was saved as unpack.log, overwriting the preexisting unpack.log) WARNING: Run 24 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName ./440000-000024-000001.dcm Run 24 ----------------------------------------- Thu May 21 10:37:42 EDT 2009 24 dti_test nii f.nii INFO: this run has an error, but trying anyway RunNo = 23 WARNING: Run 1 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName ./440000-000024-000001.dcm Are the dti scans I unpacked usable, or do I need to change my unpack command? Thanks, Jesse FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.3.1-20090521 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.1.6.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: vantz SUBJECTS_DIR: /space/ventzl/36/users/RespMon12C/subjects PWD: /space/archive/216/siemens/TrioTim-35006-20090508-140454-440000 ssh vantz setenv SUBJECTS_DIR /space/ventzl/36/users/RespMon12C/subjects cd /space/archive/216/siemens/TrioTim-35006-20090508-140454-440000

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con and sig
by adrzezga＠nmr.mgh.harvard.edu 20 May '09

20 May '09

Dear All I have 2 specific question regarding transfer of SPM-results to Freesurfer and vice versa: 1.) I transfer SPM result images (con_00x images) to freeSurfer for illustration purposes. Conversion of the images using mri_vol2surf works nicely. Now I am just not sure on how to interpret the overlay in tksurfer regarding significance thresholds. Can someone advice me on how to "translate" the Min and Max-values in the "configure overlay display" tool into actual p-values, when using SPM-generated con-images ? 2.) The second question is probably related to 1.) Can I perform a direct correlation analysis between FreeSurfer-derived results (sig.mgh) and SPM-generated results (con_00x.img), i.e. are the values in the two image types comparable or do they have to be normalized to some common ground before actual correlation analysis can be carried out ? Thanks for any advice ! Alex Alexander Drzezga, MD Visiting Assistant Professor Harvard Medical School Massachusetts General Hospital/ Athinoula A. Martinos Center for Biomedical Imaging Building 149 13th Street, Room 2301 Charlestown, Massachusetts 02129 Tel: 617 378-1071 Fax: 617 726-7422 email:adrzezga@nmr.mgh.harvard.edu

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question abt inflated brain registration
by Ritobrato Datta 20 May '09

20 May '09

Hello All, I am new to freesurfer. Is there a method to create a "registered inflated brain" from the lh.sphere.reg (which if I understood correctly, is the ?h.sphere data for a subject registered to the spherical atlas). If yes, is it also possible to display the corresponding functional data on this "registered inflated brain" ? Please let me know. Thanks Ri Ritobrato Datta, Ph.D. Post Doctoral Fellow Department of Neurology University of Pennsylvania School of Medicine 3rd Floor Gates Building 3400 Spruce St. Philadelphia Pa 19104

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new release?
by Sebastian Moeller 20 May '09

20 May '09

Dear FeeSurfer team, I just realised that a new version appeared on the Download site. Does this include the fix for the fix for the MACOSX mri_normalize? Does freeview now work on the mac? One more thing, it would be marvellous if new releases could be announced on the freesurfer list to alert the users. Thanks for developing & supplying these great tools -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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Guideline to process high resolution data using FreeSurfer and some questions
by Falk Lüsebrink 20 May '09

20 May '09

Hi FreeSurfers, Due to an accident and after several hundreds of hours of work I was finally able to completely (actually not completely, but it seems to work) process high resolution data with an isometric voxel size of 0.6mm without any manual intervention, while using the advantage of all atlases. I would like to share my experience with you and especially would like to know if and how some of my individual changes to the recon-all stream may affect the results. The data I used was acquired at 7T (Siemens), so my volumes were not very homogenous. To get rid of most of the inhomogeneities we are using a method at our lab in which two volumes are acquired, a MPRAGE and 3D gradient echo. Both volumes are co-registered and afterwards the MPRAGE is divided by the 3D GE. Everything further has been done directly using FreeSurfer. First you need to run recon-all autorecon1 cm noskullstrip s <your subject>. Using the cm flag the volumes are not conformed to 1mm^3 voxel size and 256^3, but to the smallest voxel size (in my case 0.5990mm^3 and 385^3). It is crucial to not run skullstrip using the high resolution data as this will not work! You need to go to your subject/mri folder and use mri_convert cs 1 nu.mgz nu.conformed.mgz, this creates a conformed version of the nu.mgz. Now you should run mri_em_register skull nu.conformed.mgz $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta. This has to be done using a conformed nu.mgz as in the following stage mri_watershed seems to conform the input file (Will it be really conformed? The output volume doesnt suggest this.) and if the talairach_with_skull.lta is created using a not conformed volume one gets an error stating that the WM intensity is lower than CSF intensity and the stage is exited. The nu.conformed.mgz is only used during this stage, so your high resolution volumes will never (Never? At least the output volumes are not.) be resampled, conformed or whatever to a lower resolution. After this has been done, one can use recon-all skullstrip s <your subject> and take advantage of the atlas! Though the input volume (T1.mgz) seems to be conformed during mri_watershed, the output volume (brainmask.mgz) will have the correct resolution. If the brainmask.mgz doesnt look well, try adding the wsatlas switch first, as this improved the skull stripping if only really small bits of skull and dura were still left or small pieces of the temporal lobe or cerebellum were cut off. If this doesnt help much adjust the watershed threshold using the wsthresh <value> switch (but still use wsatlas) like described in the wiki. Now run recon-all gcareg canorm careg careginv rmneck skull-lta calabel s <your subject>. Even though the aseg.mgz should look perfectly fine, one needs to stop here, as the normalization2 stage can be run only if the aseg.mgz is conformed (Why does it need to be conformed?). This is something you dont want, so go to the subject/mri folder again and run mri_normalize mask brainmask.mgz norm.mgz brain.mgz. Right now I'm running the missing stages of -autorecon2 (being at the -fix stage which will take some time) and I think it should work totally fine. Maybe the following stages using the aseg.mgz might not run as those maybe want the aseg.mgz to be conformed as well, but I don't know yet. Additionally in my case this wouldn't be a problem as I just want to measure the cortical thickness. I would highly appreciate if you could answer the questions in the brackets and how the results might be effected by the changes I have done. By the way, I tried running mri_nu_correct.mni using the T1.mgz as the input volume and running mri_normalize again afterwards to improve the inhomogeneity correction. The result looks very good, but parts of the skull and dura are not erased during the skull stripping stage (as they seem to match the intensities of GM and WM). If I adjust the watershed threshold so these are erased, pieces of the cerebellum and temporal lobes are erased additionally. Would it be possible to run mri_nu_correct using the brainmask.mgz as input volume and mri_normalize afterwards, so the inhomogeneity correction can be further improved? Will mri_nu_correct.mni work fine on a volume without skull? Thanks in advance, Regards, Falk

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brainmask volume greater than ICV
by Martin Kavec 20 May '09

20 May '09

Hi, I am running FS-4.3.0 and after recon-all -all, I am finding in aseg.stats of quite a few of my subjects that brain mask volume (1735600 mm^3) is greater than ICV (1701891 mm^3). The talairach failure detection passed fine: talairach.xfm OK (p=0.7556, pval=0.6675 >= threshold 0.005 ). The segstat step passed fine, with atlas_icv (eTIV) = 1701891 mm^3 (det: 1.144671). However, the mris_volmask, which followed right after the segstat exited with errors and dumped the core. I see this on about 30% of my analyzes. :( I can provide the data, if that could help. Thanks, Martin

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Re: Freesurfer Digest, Vol 63, Issue 35
by Sebastian Moeller 19 May '09

19 May '09

Hi Falk, what about you change the voxelsize to 1 mm before opening the volume in tkmedit for modifications and then change them back to the original values after you are done. I have not tried that, but it should work at least around the tkmedit problem... ahoi Sebastian On May 19, 2009, at 2:46 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 3 > Date: Tue, 19 May 2009 11:46:00 +0200 > From: Falk L?sebrink <falk.luese(a)gmx.net> > Subject: RE: [Freesurfer] mri_fill > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <002801c9d866$9e0fcff0$da2f6fd0$@luese@gmx.net> > Content-Type: text/plain; charset="iso-8859-1" > > As mentioned in the first email somehow tkmedit seems to skip some > slices if > one tries to edit them manually and the resolution of the volume is > not > 1mm^3. Attached is a screenshot of the filled.mgz which I tried to > edit on > the left from the coronal view and on the right from the sagittal > view. > > The resolution of the volume used in this case is 0.6mm. If I use the > "Slice" thing to browse through the slices nearly every second slice > is > skipped. Increasing or decreasing the volume index by 1 in the > direction I > would like to move on doesn't work either. For example if I change the > volume index from 162 338 124 to 163 338 124 the same slice is being > shown. > 161 338 124 and 164 338 124 are different as it should be, but it is > not > possible to view 163 and so it is impossible to edit this slice. > > Are there any other tools available to edit volumes like tkmedit > does? It > doesn't need to be included within FreeSurfer but it would be better > if it > could handle the .mgz format. > > Regards, > Falk -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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