Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 discussions

Rejoindre mon réseau sur LinkedIn
by Jamaan Alghamdi via LinkedIn 09 Jul '11

09 Jul '11

LinkedIn ------------ Jamaan Alghamdi souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Jamaan Alghamdi http://www.linkedin.com/e/-qq80um-gpx7oboi-9/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59… Voir l'invitation de Jamaan Alghamdi http://www.linkedin.com/e/-qq80um-gpx7oboi-9/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59… ------------------------------------------ SAVEZ-VOUS que vous pouvez utiliser votre profil LinkedIn comme page Web personnelle ? Personnalisez l'adresse Web de votre profil et utilisez-la sur vos cartes de visite, comme signature d'e-mail, sur votre site, etc. http://www.linkedin.com/e/-qq80um-gpx7oboi-9/ewp/inv-21/ -- (c) 2011, LinkedIn Corporation

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Rejoindre mon réseau sur LinkedIn
by Jamaan Alghamdi via LinkedIn 09 Jul '11

09 Jul '11

LinkedIn ------------ Jamaan Alghamdi souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Jamaan Alghamdi http://www.linkedin.com/e/-qq80um-gpx7h7cg-28/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Jamaan Alghamdi http://www.linkedin.com/e/-qq80um-gpx7h7cg-28/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ SAVEZ-VOUS que vous pouvez utiliser votre profil LinkedIn comme page Web personnelle ? Personnalisez l'adresse Web de votre profil et utilisez-la sur vos cartes de visite, comme signature d'e-mail, sur votre site, etc. http://www.linkedin.com/e/-qq80um-gpx7h7cg-28/ewp/inv-21/ -- (c) 2011, LinkedIn Corporation

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Optseq with Sparse Sampling
by Sam Norman-Haignere 08 Jul '11

08 Jul '11

Hi, I'm planning to run an auditory experiment using a pseudo-sparse sampling design. Something like: 4 sec stim period + 2 sec acquisition + 4 sec stim period + 2 sec acquisition ... So for example, I'd like to find an optimal sequence for a design with a TR of 6 seconds but where the stimulus presentations can only occur in specific 4 second intervals after acquisition. There is room for jittering either in which 4-sec periods are NULL or alternatively in which part of the 4 seconds is occupied by stimulus (e.g. 3 sec stim + 1 sec NULL). Is there a way to use optseq for this type of design? For example, maybe you could specify when half of the NULL conditions occur. Thanks, Sam Norman-Haignere

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muliple fressurfer instance and cuda
by Knut J Bjuland 08 Jul '11

08 Jul '11

Hi When I have ran two or more Freesurfer instance in pc with one geforce gtx 460. I usually get a abort or memory corruption when running two or more Freesurfer instance. I usually get trouble when two ore more Freesurfer instance is in autocon3 phase of the recon-all protocol. Cheers Knut J

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Freesurfer and VBM
by Ahmed, F, Me <fahmed＠sun.ac.za> 08 Jul '11

08 Jul '11

Hello, I'm wondering if anyone could help me out with a question I had. For a study I'm working on, I'm comparing the regional brain volumes in adolescents with and without PTSD. I ran VBM analysis and Freesurfer on my subjects and I found some significant results on VBM (however, only using uncorrected p values) and on Freesurfer, I found no group differences in brain regions. Is there an explanation for that? If anyone has any thoughts I'd really appreciate it. Thank you kindly! Fatima

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Errors with Multiple Frames
by Antonella Kis 08 Jul '11

08 Jul '11

Hi Bruce, My LNX3 the only one which is working is a Fedora Linux, Kernel Linux 2.6.32.23-170.fc12.x86_64, GENOME 2.28.2 LNX2 where I get the weird surface display is a Linux CENTOS x86_64, GENOME 2.16.0 The Analyst computer is a Linux, Kernel Linux 2.6.35.13-91.fc14.x86_64, GENOME 2.32.0 I will contact Allison and thank you for the information. Also, I promise will be the last question from me for today: when I am doing my data analysis after running the recon -all and qcache -all for my subjects, what is the best steps order to be followed. While reading the FreeSurfer Troubleshooting Reconstruction Work suggests the user to run all these steps at once before beginning to inspect the data since this allows the user to see the final complete output before deciding on any interventions.But this steps are in a different order that the one in the tutorial and also in a different order that the one described in the attached document. Please advise. Thank you and have a great day! Antonella ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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Re: [Freesurfer] cortical dysplasia
by Carolina Valencia 08 Jul '11

08 Jul '11

Hi Pedro, I tried to send you the image of my problem but the mailing list rejected my attachment, despite the file is only 769 k. How I can post an image in order to illustrate my problem? Thanks, Carolina 2011/7/7 Carolina Valencia <cvalencia(a)linkdx.com.co> > Hi Pedro, > > Yes I have a case with heterotopia in the left hemisphere , I enclosed the > image. I save the point in question (the gray matter region within white > matter) in tkmedit and open it in tksurfer to know the thickness, for this I > ask if FS takes into account the embedded region of the grey matter to > measure the cortical thickness? > > Thanks a lot, > > Carolina > > 2011/7/7 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> > >> Carolina, >> >> We have worked with several cases of MCD (including cortical dysplasia). >> We have published this paper: >> https://surfer.nmr.mgh.harvard.edu/pub/articles/jon_372_LR.pdf >> >> It may help. >> >> But in most cases of cortical dysplasia (not Gray matter >> heterotopia cases) you'll find a ticker cortex not a thinner one. But maybe >> you could post one image illustrate this problem. >> >> PPJ >> >> >> >> >> On Thu, Jul 7, 2011 at 10:39, Carolina Valencia <cvalencia(a)linkdx.com.co>wrote: >> >>> Hello FSexperts >>> >>> I have a MPRAGE image of cortical dysplasia, I have some regions of grey matter within the white matter, and I measured the cortical thickness in the projections of those regions and I expected to find a thinnercortex instead I found a cortical thickening. FS takes into account the embedded region of the grey matter to measure the cortical thickness? >>> >>> Best regards, >>> >>> Carolina >>> >>> _______________________________________________ >>> 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. >>> >>> >> > > > -- > -- > *Carolina Valencia Muñoz* > Bioingeniera > *LINK DIAGNOSTICO DIGITAL SA > *Cel: 3016411824 > Of: (4) 444 54 65 > -- -- *Carolina Valencia Muñoz* Bioingeniera *LINK DIAGNOSTICO DIGITAL SA *Cel: 3016411824 Of: (4) 444 54 65

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Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 30
by Antonella Kis 08 Jul '11

08 Jul '11

My LNX3 the only one which is working is a Fedora Linux, Kernel Linux 2.6.32.23-170.fc12.x86_64, GENOME 2.28.2 LNX2 where I get the weird surface display is a Linux CENTOS x86_64, GENOME 2.16.0 The Analyst computer is a Linux, Kernel Linux 2.6.35.13-91.fc14.x86_64, GENOME 2.32.0 I will contact Allison and thank you for the information. Also, I promise will be the last question from me for today: when I am doing my data analysis after running the recon -all and qcache -all for my subjects, what is the best steps order to be followed. While reading the FreeSurfer Troubleshooting Reconstruction Work suggests the user to run all these steps at once before beginning to inspect the data since this allows the user to see the final complete output before deciding on any interventions.But this steps are in a different order that the one in the tutorial and also in a different order that the one described in the attached document. Please advise. Thank you and have a great day! Antonella ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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Error with multiple frames
by Antonella Kis 08 Jul '11

08 Jul '11

Hi Bruce, Sorry for making you confused. The true is I have 3 computers in my office. On two of them (LNX2 and LNX3) I installed by myself the new version of the FS. LNX2 is the one on which the bert infalted surface is looking weird. LNX3 is working perfect ( I cross my fingers and hope nothing bad will happen. I need to get some results ASAP). On the third computer called Analyst was installed the new FS version by somebody else. This is the computer on which I get the ERROR with the multiple frames. Hopping that you will not be even more confused I will be very grateful if you have any suggestion, to help me eliminate this error and to be able to run the recon-all on this computer. PS. Is there any space available for the September course? Are you guys gone present this course sometimes in Toronto? Many thanks. Antonella ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 30
by Antonella Kis 08 Jul '11

08 Jul '11

Good morning Bruce, And many thanks again. Yes, bert inflated looks OK on the other computer. I will try to update the video card driver and see if this will fix the problem. In the mean time I have one more question: while running the recon-all on a new computer hhttps://kidmail.sickkids.ca/owa/?ae=PreFormAction&a=Reply&t=IPM.Note&id=RgAAAAAkiCYl32zeSa5LWUu0M8WhBwBZqTK0%2fPR%2bQJ%2b1OIUDJtvhAAAAt2gIAABZqTK0%2fPR%2bQJ%2b1OIUDJtvhAAAAt5XmAAAJ&pspid=_1310134871973_963068284#aving installed the v.5.1 version of FS I am getting an error: Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/june2011/_orig_/NPI001/mri/orig/001.mgz has frames Do I need to unzip my NPI001.nii.gz file? But even if I do this I will get the same error. Do I need to convert the file in a .lta file? Can you please advise me? Thank you very much and have a great day! Antonella ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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Freesurfer July 2011