Freesurfer

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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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mri_glmfit DOF error
by matteo.diano＠tiscali.it 08 Jul '11

08 Jul '11

Hello Freesurfers, I have a problem with mri_glmfit. I performed the analysis on two FA data. My fsgd is: GroupDescriptorFile 1 Title SUBJ_FA Class PRE Class POST Input FA_1 PRE Input FA_2 POST group_difference.mtx: 1 -1 The results in cmd line DOF = 0 ERROR: DOF = 0 What does it mean this error? Thank you for your help. Matteo Non temiamo alcun confronto: Tiscali ha l'Adsl più veloce d'Italia!Risparmia con Tutto Incluso Light: Voce + Adsl 20 mega a soli 17,95 € al mese per 12 mesi.http://abbonati.tiscali.it/telefono-adsl/prodotti/tc/tuttoincluso_light/?WT.mc_id=01fw

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Re: [Freesurfer] Freesurfer and VBM
by Ed Gronenschild 08 Jul '11

08 Jul '11

Hi Fatima, Your findings are not surprising. There is plenty of literature describing problems with the VBM technique. You may read e.g., Kennedy et al (2009), Neurobiology of Aging, vol. 10, 1657-1676 and references cited herein. Ed On 8 Jul 2011, at 15:02, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > 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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make_average_subject error
by leonardo kay 08 Jul '11

08 Jul '11

Hi all Could anyone help me with this error: MRISreadAnnotationIntoArray: vertex index out of range: 1499028058 i=5A595959, in_array_size=133467 annot file: /home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot This appeared after trying to average my subject data. It says ' vertex index out of range '. All acquisitions were made using the same parameters so I don't know what this may mean. Thanks in advance -- Leo Kay.

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A question about the Freesurfer version compatibility of Tracula
by Shanqing Cai 08 Jul '11

08 Jul '11

Hi, I am using Tracula, a new tool that comes with version 5.1.0 of FreeSurfer. However, my data set are processed with the recon-all of an earlier version of FreeSurfer: 5.0.0. I wonder whether I need to rerun recon-all on all the subjects in the data set with 5.1.0. Would running Tracula on 5.0.0 reconstructions cause any problems that render the results unusable/not trustable? Thank you! Best, Shanqing Cai

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Retinotopy stimuli
by Anders Hougaard 08 Jul '11

08 Jul '11

Dear freesurfers, Which stimuli do you think provide the best retinotopic maps? I have done a retinotopy analysis using the following stimuli: Polar angle: - 45 deg counter-clockwise rotating wedge - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Eccentricity: - expanding ring - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Any suggestions on how to optimize this stimulation? E.g. different period length, more runs, bi-directional, different TR Thank you! Best regards, Anders

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