Freesurfer November 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
127 discussions

retinotopic mapping with bowtie vs. wedge
by Y.V. Jiang 22 Nov '10

22 Nov '10

Dear Doug and other Freesurferers, We are considering using rotating bowtie-shaped stimuli rather than rotating wedges for retinotopic mapping. The bowties are essentially two symmetriccal wedges, but unlike horizontal/vertical meridian mapping, they do rotate around (rather that stay at horizontal/vertical meridian). Is Freesurfer's retinotopic mapping program capable of handling data analysis of bowtie retinotopy? Do we need to make changes to the analysis stream (e.g., when entering the number of cycles, should this be twice as frequent?) Would this mess up with color maps? Thanks for your feedback. -Yuhong ---------------------------------------------------------- Yuhong Vanessa Jiang, PhD, Department of Psychology, Univ of Minnesota jiang166(a)umn.edu, 612-625-7003 ----------------------------------------------------------

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severe recon-all errors only in v5.0
by Andreas Berger 22 Nov '10

22 Nov '10

Hello Surfers, we just finished processing our subjects (recon-all -all) with freesurfer version 5.0. In 16 out of 240 subjects i found severe errors: in about 4 of them the surface looks damaged (see attached screenshot1), in the others the skullstrip didn't work, in one case gnawing away some brain (see attached screenshot2), in the others there's too much skull left, the surface seems ok though (screenshot3). all of the 16 subjects looked fine with version 4.5. is this a known issue? by the way, recon-all reported no errors on any of them. will keep using v4.5 for now. thanks, andreas -- Andreas Berger <n0642496(a)students.meduniwien.ac.at>

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How to add volume to the pial surface?
by xuemei lei 22 Nov '10

22 Nov '10

Hi I have ran the recon-all using Freesurfer 5.0 version. And I found some GM tissue exluded from GM in temporal lobe like in the attached figure.I want to know how to fix these problems. Since the page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits has showed how to delete volume which is really useful, however, we faced the opposite problem, that is how to add volume. Thanks in advance！ -- Xuemei Lei National Key Laboratory of Cognitive Neuroscience and Learning<http://psychbrain.bnu.edu.cn> Beijing Normal University Beijing, China. 100875 Tel: +86-13269171259 ============================================== Welcome to visit my blog: www.mobiye.com

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Re: [Freesurfer] volumetry of PSP related structures...
by antonio cerasa 22 Nov '10

22 Nov '10

Dear Gonzalo If you need to perform invidual evaluation I suggest you to consider the MR imaging index made by Prof. Quattrone (Radiology 2008, 246(1): 214-221). Overall, our FS results highlighted the role of thalamic atrophy in the patients with PSP. ----- Original Message ----- From: "Gonzalo Rojas Costa" <gonzalo.rojas.costa(a)gmail.com> To: <a.cerasa(a)isn.cnr.it> Sent: Saturday, November 20, 2010 10:24 PM Subject: Re: [Freesurfer] volumetry of PSP related structures... Hi: Which evidence you confirmed ?... you did the analysis of the volumetry of which structure ?... Culd you please send me the abstract of your work ?... I have a patient with PSP, and I processed the volumetry wirh freesurfer, but I don't know which structure must be studied... Sincerely, Gonzalo Rojas Costa El 20-11-2010 3:05, a.cerasa(a)isn.cnr.it escribió: > Dear Gonzalo > We've a PSP-freesufer paper in revision on Parkinsonisms and Related > Disorders. > In this particular population FS confirms evidence provided by previous > VBM studies. > > ----- Original Message ----- > From: Gonzalo Rojas Costa > To: freesurfer(a)nmr.mgh.harvard.edu > Sent: Fri, 19 Nov 2010 18:14:38 -0300 > Subject: [Freesurfer] volumetry of PSP related structures... > > Hi: > > How can I get the volume of pons, middle cerebellar pedunclues, > superior cerebellar peduncles ?... And, there exist any PSP-Freesurfer > related paper ?... > > Sincerely, > > -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl -- This message was scanned by ESVA and is believed to be clean. Click here to report this message as spam. http://smtp.isn.cnr.it/cgi-bin/learn-msg.cgi?id=0A23C28025.09A60

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handles in the non-cortical regions, does it matter?
by xuemei lei 21 Nov '10

21 Nov '10

Hi, I have ran the recon-all, and got some handls in the non-cortical regions caused by the islands in C140-150 slices, and I am just interested in the cortical regions. I don't want to fix it. I want to know whether it matters or not。 Thank you for help -- Xuemei Lei National Key Laboratory of Cognitive Neuroscience and Learning<http://psychbrain.bnu.edu.cn> Beijing Normal University Beijing, China. 100875 Tel: +86-13269171259 ============================================== Welcome to visit my blog: www.mobiye.com

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handles in the non-cortical regions, does it matter?
by xuemei lei 21 Nov '10

21 Nov '10

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qcache
by Dhinakaran Chinappen 20 Nov '10

20 Nov '10

Dear Freesurfer(ers). Quick ques: is it possible to run recon-all with the qcache flag during the initial reconstruction, as opposed to re-using recon-all with the qcache flag afterwards? Thanks, Dhinakaran.

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Re: [Freesurfer] volumetry of PSP related structures...
by a.cerasa＠isn.cnr.it 20 Nov '10

20 Nov '10

Dear Gonzalo We've a PSP-freesufer paper in revision on Parkinsonisms and Related Disorders. In this particular population FS confirms evidence provided by previous VBM studies. ----- Original Message ----- From: Gonzalo Rojas Costa To: freesurfer(a)nmr.mgh.harvard.edu Sent: Fri, 19 Nov 2010 18:14:38 -0300 Subject: [Freesurfer] volumetry of PSP related structures... Hi: How can I get the volume of pons, middle cerebellar pedunclues, superior cerebellar peduncles ?... And, there exist any PSP-Freesurfer related paper ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- This message was scanned by ESVA and is believed to be clean. Click here to report this message as spam. http://smtp.isn.cnr.it/cgi-bin/learn-msg.cgi?id=5B9DE28046.8BE5A

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recon1: brain missing
by suzanne oosterwijk 19 Nov '10

19 Nov '10

Hi, I have been running recon1 recently and I have noticed that for some of my participants big chunks are missing in the brainmask.mgz. Out of 20 participants, five participants have this problem. The pattern is similar across participants: the missing parts start around slice 70-50 at the bottom (cerebellum) and then move upward. The data can be found in: /autofs/space/boggart_001/users/oosterwi/construct_struc It concerns constr011 (which I corrected using the clone method), and constr012, constr016, constr019 and constr020 (which still show the problem). I think it can be solved by cloning the T1 (aux volume) as is explained in the Freesurfer tutorial. Still, I wonder whether this is the best solution, and why this is happening in the first place. I appreciate any help or feedback on this. Thanks in advance! kind regards, Suzanne Oosterwijk -- Suzanne Oosterwijk Postdoctoral Researcher Interdisciplinary Affective Science Lab Department of Psychology Northeastern University 114 Lake Hall s.oosterwijk(a)neu.edu

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volumetry of PSP related structures...
by Gonzalo Rojas Costa 19 Nov '10

19 Nov '10

Hi: How can I get the volume of pons, middle cerebellar pedunclues, superior cerebellar peduncles ?... And, there exist any PSP-Freesurfer related paper ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Freesurfer November 2010