Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

normalized SPGR as an input for inflation
by Vadim Axel 29 Mar '10

29 Mar '10

Dear experts, I run my statistical analysis in SPM, while after coregistration I normalize my data (SPGR and EPI). Since my models and activations images are based on normalized data it's natural for me to use the normalized SPGR as an input for freesurfer inflation. Is it a good enough? Since I run inflation for each individual brain, I basically can do it for non-normalized anatomy, which is preferable, I think. However, then the coordinates are not MNI / Talariach. Attached the comparison of activations for normalized (left side) vs. non-normalized. It looks pretty similar, though the brains look of different shape. So, am I OK to do it on normalized brain? Thanks for help, Vadim

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recon-all error
by ythomas 29 Mar '10

29 Mar '10

Hi, good morning. I encountered a recon-all error in one subject: ERROR: _FindFacePath: could not find path! Linux compute-0-117.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux Interestingly, the error does not show up in the recon-all.error file but does so in the recon-all.log file. You can find the failed subject here: /autofs/space/terrier_002/users/ythomas/GSP/failed_FS_subjects/ 090620_JG49ZK_FS Thanks, Thomas

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tksurfer: more than one overlay with "-overlay" switch?
by John Gelburg 27 Mar '10

27 Mar '10

Hi, I would like to load from the command prompt several overlays, each one for separate layer. I tried just to use twice -overlay switch, but only the last overlay was loaded. Is it feasible? Thanks, John

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calculate the average thickness of a ROI around PCC
by Guang Zeng 26 Mar '10

26 Mar '10

Hi, there, I'd like to measure the average thickness of a ROI around PCC (posterior cingulate cortex). I only have its MNI152 coordinate (-2, -45, 34). How can I calculate its corresponding RAS and Talaraich coordinate, is there an equation? Thanks! Guang _________________________________________________________________ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:…

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Re: [Freesurfer] Freesurfer Digest, Vol 73, Issue 64
by Gonzalo Rojas Costa 26 Mar '10

26 Mar '10

Hi Andreas: As far as I know, the complete command is: recon-all -s subjid -skullstrip -no-wsgcaatlas -wsthresh 35 -clean-bm Sincerely, Gonzalo Rojas Costa Laboratory of Medical Imaging Processing Department of Radiology Clínica Las Condes Santiago Chile > Date: Fri, 26 Mar 2010 11:07:01 +0100 > From: Andreas Berger <andreas.berger.01(a)gmail.com> > Subject: [Freesurfer] changing watershed threshold has no effect > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <68f948a91003260307g4fee4b69s9c04624544df29a1(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > hello freesurfers, > > we are having a problem with insufficient skull stripping, in 66 out > of 200 subjects this affects the pial surface, as can be seen in the > attached screenshot1. since the problem is somewhat generalized in > location, i tried to change the watershed threshold as suggested by > the wiki. i tried the values 20, 15, 10, 5, 0 (recon-all -all -clean > -wsthresh n), but even 0 seems to have no effect (it looks different, > but not less skull), see screenshot2. am i doing it wrong?

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Poor Talairach registration and effect on ICV
by Martin Kavec 26 Mar '10

26 Mar '10

Hi, in our population of MCI patients, unfortunately parts of the cerebellum were not completely scanned. I ran the data throught the whole FS-4.5.0 pipeline and I see that the eTIV normalized volumes of the segmented structues have very large variance compared to the eTIV normalized group of independent age matched subjects with the full brain coveage. I assume that this is possibly due to the suboptimal registration to the template, which is used to compute eTIV. In fact, all the subjects with incomplete cerebellum failed to pass the quality check of the registration to Talairach, but on the first glance the registration seemed fine to me so I just used -notal-check flag to complete recon-all -all. I know I could go back, check more carefully and correct the Talairach transform manually, but I hesitate to go this way. Rather I thougt if it would be possible/feasible to remove the cerebellum from each subject AND the template and possibly achieve better registration from these images. Thanks in advance for opinions, Martin

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changing watershed threshold has no effect
by Andreas Berger 26 Mar '10

26 Mar '10

hello freesurfers, we are having a problem with insufficient skull stripping, in 66 out of 200 subjects this affects the pial surface, as can be seen in the attached screenshot1. since the problem is somewhat generalized in location, i tried to change the watershed threshold as suggested by the wiki. i tried the values 20, 15, 10, 5, 0 (recon-all -all -clean -wsthresh n), but even 0 seems to have no effect (it looks different, but not less skull), see screenshot2. am i doing it wrong?

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Skipping time consuming FS parts.
by Mohammed el Morabit 26 Mar '10

26 Mar '10

Dear FS experts, I have a large data set which I want to recon-all, in order to obtain the cortical, sub-cortical parcellations and the corresponding volumes and thicknesses. As the reconstruction is very time-consuming I was wondering which steps I might skip without significant decrease in quality of the cortical segmentation. I noticed for instance that the automated topology fix takes quite long - if I skip this part, how does that change my results? Thanks in advance. Mohammed.

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Current age or Age of onset
by 류철형 25 Mar '10

25 Mar '10

Dear All I'm trying to search for the cortical thickness change associated with the progression of a neurodegenerative disease. Each patient may have current age, age of onset, disease duration, and disease severity score. To find the cortical areas in which cortical thickness is correlated with the disease duration, Which variable do I have to choose as a covariate? Current age or Age of onset? It may be simple question and 'current age' may be the answer. But, because the current age is the sum of duration and age of onset, we can make the regression equation, Y (thickness) = a*A (onset age) + b*B (duration) + e (error). In my study, the result from qdec was better when the onset age was selected as covariate. I'm waiting for your advice. Chul Hyoung Lyoo

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Creating a distance scale bar for a pial surface-render viewed in tksurfer
by Eric Moulton 25 Mar '10

25 Mar '10

I was wondering if freesurfer has a way of generating a scale for distance, similar to what one would see in the legend of a roadmap. I'm thinking of using such a scale for a 3-d pial surface-render of an averaged brain (as generated using make_average_surface). Since it's a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale, with scale bars for the x, y, and z directions. Does freesurfer have some visual representation of a distance scale like I've described, or perhaps some alternative? Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772

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