Freesurfer July 2008

freesurfer@nmr.mgh.harvard.edu

55 participants
74 discussions

Re: [Freesurfer] FS processing of FTLD subjects
by Sky Raptentsetsang 16 Jul '08

16 Jul '08

Hi Bruce, Yes there is a major inhomogeneity issue that we deal with prior to running FS, along with an addition skull strip step. With all of our 4T data, because of the large bias field and hyper-intense Dura Matter, we perform a bias correction and skull-strip before the data is entered into FS. During these pre-processing steps we think that some orientation information is lost due to multiple format conversions. Forgive me but I am introducing other issues, but because of this loss of positional information I cannot reliably optimize the talairach transformation in tkregister2 (see attached picture). You will see that the reference point in the FOV of tkregister2 is in the wrong quadrant. Though from what I can see the talairach transforms seem to be good, but some appear to be slightly underestimated. So maybe this is probably a good target to try and fix the underestimation of our surfaces. This problem with viewing the talairach has never sat well with me, but the surfaces and segmentations in our other studies look good despite this issue. Is there a way to reset the FOV in tkregister so that I can reliably correct any slight errors in the talairach transform to see if this can fix what were seeing with this subject group? When I add control points in the area where wm should be, the segmentation that usually results includes anterior carotid artery or lots of the small pieces of dura that I was unable to threshold out. Our next option is to simply edit all non-brain tissue around these areas of atrophy, but if there is any other relatively less time consuming option then it would be much appreciated. Sky At 12:52 PM 7/16/2008, Bruce Fischl wrote: >Hi Sky, > >hard to tell from just the one slice. Is there a big bias field in the >data? Have you tried adding control points in the wm that you lose? > >cheers, >Bruce > >On Wed, 16 Jul 2008, Sky Raptentsetsang wrote: > >>Hello Surfers, >> >>I am trying to FreeSurfer process a group of subjects from our Frontal >>Temporal Lobar Dementia project that were scanned on our 4T Siemens MRI. >>So far this endeavor has only created long hours of edits due to the >>absence of any visible White Matter in the Frontal and/or Temporal Poles. >>I have included a couple pictures of FS surface estimate on two of our >>many problematic subjects. >>I am wondering if you have any solutions or input to help FS include >>these regions of great atrophy. >> >>Thanks in advance for any input on this tedious issue. >> >>Sky R.

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Question about FreeSurfer citation
by Pedro Paulo de Magalhães Oliveira Junior 16 Jul '08

16 Jul '08

Hi, Some time ago I have asked a question similar to this and the answer was a page with a template: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation I would like to ask two questions: 1) Is this template a copy paste one? 2) Is there any concern regarding plagiarism using this template? I mean even if we make subtle changes, could the editor refuse the paper based on the fact we are using a material and methods based on a text model? Thanks, Pedro Paulo Oliveira Jr

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FS processing of FTLD subjects
by Sky Raptentsetsang 16 Jul '08

16 Jul '08

Hello Surfers, I am trying to FreeSurfer process a group of subjects from our Frontal Temporal Lobar Dementia project that were scanned on our 4T Siemens MRI. So far this endeavor has only created long hours of edits due to the absence of any visible White Matter in the Frontal and/or Temporal Poles. I have included a couple pictures of FS surface estimate on two of our many problematic subjects. I am wondering if you have any solutions or input to help FS include these regions of great atrophy. Thanks in advance for any input on this tedious issue. Sky R.

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volumes in wmparc.stats vs. aparc.stats
by Marin Richardson 15 Jul '08

15 Jul '08

Hi all, I noticed that the gray volumes for parcellated cortical regions in wmparc.stats are different from those for the same region in aparc.stats (e.g. ctx-lh-middletemporal = 8419 in wmparc.stats, middletemporal = 9466 in lh.aparc.stats). Why are the values different and which one is a better measure to use? Thanks, Marin Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Lateral ventricles not filled entirely
by Dorit Kliemann 15 Jul '08

15 Jul '08

Hi, I recently started using freesurfer and finally processed my first subjects with all three recon steps (using the latest version). Checking the white matter volume I recognized that all my scans have the same issue: The lateral ventricles aren't filled entirely but there are some black spots within the ventricles..in the tutorial is written that one should handle this in a described way but I was wondering if this is necessary when recon3 was sucessful without any errors..... Does anyone have experience with that? (see attached picture) Thanks a lot, Dorit Kliemann

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percent signal change
by Elif SIKOGLU 14 Jul '08

14 Jul '08

Hello. I obtained the percent signal change using roisummary-sess. (divided the BOLD amplitude by the mean functional baseline offset to get the percent signal change.) Is there a way to get an error estimate (i.e. standard deivation) on this value? Thanks Elif

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Statistical question
by Juergen Haenggi 14 Jul '08

14 Jul '08

Dear FS experts Does it make a difference whether I introduced the flag doss already in mris_preproc or only later when using mri_glmfit? In mris_preproc the flag doss after the fsgd file is not recognized (see below) mris_preproc --fsgd GCS_FSGD_lh_thickness.txt doss --target average --hemi lh --meas thickness --out GCS_lh_thickness_cov_doss.mgh ERROR: flag doss not recognized [Macintosh-3:average/stats/glm] juergenhaenggi% I used FS 4.0.5 for Mac Intel Thanks for help Regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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mri_watershed Error: Problem with WM_HALF_MIN too small
by Gonzalo Sanchez Benavides 14 Jul '08

14 Jul '08

Dear FS experts, When I run recon-all, one of my subjects get this error in mri_watershed process: *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=121 y=125 z=133 r=78 first estimation of the main basin volume: 2032411 voxels mri_watershed Error: Problem with WM_HALF_MIN too small Can you tell me what's wrong? The input image seems to be good enough. Thank you very much for your answers and for this excellent software -- Gonzalo Sánchez Benavides

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recon difficulties
by nils rettby 11 Jul '08

11 Jul '08

There seems to be two problems with the recon. First the pia seems to be intruding into the white matter Then in the other hemisphere there seems to be a hole in the white matter Is there a way to fix this? Please see attached pictures Thanks for your help

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How to show one-tailed t-contrast?
by Juergen Haenggi 11 Jul '08

11 Jul '08

Dear FS experts We have done some FS analysis and would like to show only only the positive contrast. How to do this? We have already run mri_glmfit. Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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Freesurfer July 2008