Re: [Freesurfer] FreeSurfer use in dogs
Thanks Nick Bruce, Nick - I have high resolution T1W 3D scans, with 1mm voxel size and pretty good grey white matter contrast. Could you put me in touch with those that have used freesurfer on canine brains please? If I had a canine brain MRI atlas, similar to the Talairach atlas, could I integrate this into Freesufer and use this as my template instead? Bruce - how do I go about trying the 'monkey stream'? With thanks, Marjorie. From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, 6 July 2011 11:36 PM To: Marjorie Milne Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer use in dogs Hi Marjorie, I don't know of anyone who has used it in dogs, but you could try the monkey stream and see if it works for you (it will disable all the human-specific atlases and such). It will require more manual intervention though cheers Bruce On Wed, 6 Jul 2011, Marjorie Milne wrote: Hello Freesurfers, I would like to use FreeSurfer to analyse brain morphology in dogs but do not know if the techniques can be applied in this species. Does anyone have experience using FreeSurfer in dogs, and any tips to get the techniques to work? Regards, Marjorie Milne ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Retinotopy stimuli
Hi all, Thank you very much! I did 2 runs of each of the stimuli I described in one session (I previously got some pretty decent maps from these data using the mrVista package from Stanford). I followed the retinotopy instructions from the FS wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis) but the results did not make much sense. I guess I need to use some other commands or change some parameters in order to view reasonable eccentricity and polar angle maps. I have not managed to find any other documentation on how to do this. This is what my raw angle looks like: http://dl.dropbox.com/u/6981172/raw_angle.tif Best, Anders 2011/7/7 Jonathan Polimeni j...@nmr.mgh.harvard.edu hi anders, the optimal set of stimulus parameters will depend somewhat on what cortical area(s) you are trying to map and on the details of your acquisition. in general, stimulating with both clockwise- and counterclockwise-rotating wedges for polar angle mapping and with both expanding and contracting rings for eccentricity mapping improves the accuracy of the maps, and the proper analysis of this data is implemented fsfast. the width of the wedge or the ring will depend on the cortical area you are trying to stimulate, but you may want to consider a thinner wedge. also, 8 Hz flickering has been shown to activate area V1 more strongly than other frequencies, and smoothly moving stimuli can also help. then, depending on your voxel size, field strength, coil array, etc., you could include more cycles and may need to average together multiple runs. marty, roger et al. have a few nice papers that i'd recommend that discuss some of these details relating to phase-encoded retinotopic stimuli. Sereno Tootell. Curr Opin Neurobiol. 2005;15(2):135-44. Tootell et al. J Neurosci. 1997;17(18):7060-78. Sereno et al. Science. 1995;268(5212):889-93. (the '97 paper discusses the ring/wedge thickness, the '95 paper discusses the advantages of using both expanding + contracting stimuli, and the '05 paper discusses the use of smoothly varying stimuli.) hope this helps. were you able to get reasonable looking maps with the stimuli you described below? -jon On Thu, 7 Jul 2011, Anders Hougaard wrote: 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 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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] A question about the Freesurfer version compatibility of Tracula
Hi Shanqing - As long as you have good aparc+aseg's for your subjects, the version should not be a problem. a.y On Thu, 7 Jul 2011, Shanqing Cai wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Freesurfer and VBM
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 ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] muliple fressurfer instance and cuda
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 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] muliple fressurfer instance and cuda
Try running only one GPU-assisted recon-all On Fri, Jul 8, 2011 at 10:02, Knut J Bjuland knut...@hotmail.com wrote: 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 ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Mri_glmfit ERROR: dimension inconsistency in source data
Hi, During running fixed effects glm to combine runs, the analysis of all but one subject went fine. The log file contains this error message: mri_surf2surf --srcsubject 1250 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 3runs/tmp.mris_preproc.63877/1250.1.mgh --sval 3runs/tmp.mris_preproc.63877/subjsurfvals.mgh --noreshape --no-cortex ERROR: dimension inconsistency in source data Number of surface vertices = 132315 Number of value vertices = 132299 I see that mri_vol2surf --src run1.feat/stats/varcope1.nii.gz --srcreg run1.feat/reg/freesurfer/anat2exf.register.dat --hemi lh --out 3runs/tmp.mris_preproc.63877/subjsurfvals.mgh --noreshape Results in creating a file with dimensions 132299 1 1. Which data source data has then 132315 vertices? How can I correct this? Thank you for your help! Best, Aga ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 30
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=PreFormActiona=Replyt=IPM.Noteid=RgAkiCYl32zeSa5LWUu0M8WhBwBZqTK0%2fPR%2bQJ%2b1OIUDJtvht2gIAABZqTK0%2fPR%2bQJ%2b1OIUDJtvht5XmAAAJpspid=_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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 30
Hi Antonella, where did you get NPI001.nii.gz? Can you send us the output of running mri_info on it? Sounds like it has more than one frame in it. What are the multiple volumes? cheers Bruce On Fri, 8 Jul 2011, Antonella Kis wrote: 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=PreFormActiona=Replyt=IPM.Noteid=RgAkiCYl32zeSa5LWUu0M8WhBwBZqTK0%2fPR%2bQJ%2b1OIUDJtvht2gIAABZqTK0%2fPR%2bQJ%2b1OIUDJtvht5XmAAAJpspid=_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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Freesurfer and VBM
Hi Ed, Thanks for that reassurance! Nice to know I didn't do something wrong! I'll have a read through of this literature, thank you so much!!! Fatima -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ed Gronenschild Sent: 08 July 2011 16:51 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer and VBM 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-requ...@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 ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_glmfit DOF error
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 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 30
now I'm confused. What computer are you running it on that does fail? On Fri, 8 Jul 2011, Antonella Kis wrote: Here is my results after running mri_info on the file NPI001.nii.gz (I can run recon-all for the same file on a different computer without getting this multiple frames error): niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm Volume information for NPI001.nii.gz type: nii dimensions: 181 x 217 x 181 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 181.000 dof: 0 xstart: -90.5, xend: 90.5 ystart: -108.5, yend: 108.5 zstart: -90.5, zend: 90.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 1., y_r = 0., z_r = 0., c_r = 0.5000 : x_a = 0., y_a = 1., z_a = 0., c_a = 0.5000 : x_s = 0., y_s = 0., z_s = 1., c_s = 0.5000 Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 1. 0. 0. -90. 0. 1. 0. -108. 0. 0. 1. -90. 0. 0. 0. 1. voxel-to-ras determinant 1 ras to voxel transform: 1. -0. -0.90. -0. 1. -0. 108. -0. -0. 1.90. 0. 0. 0. 1. Thank you. 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. ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Error with multiple frames
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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Freesurfer and VBM
Fatima, I can't really say anything on this topic but I did want to point you to some information on FreeSurfer vs. VBM: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.WhataretheadvantagesofFreeSurferoverVBM.3F Allison On Fri, 8 Jul 2011, Ahmed, F, Me fah...@sun.ac.za 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 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] cortical dysplasia
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 cvalen...@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 p...@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 cvalen...@linkdx.com.cowrote: 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@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 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Freesurfer and VBM
There are a couple of things that come to mind. - Are you sure you have the same GLM in both analyses? - It might not be the thickness that is changing. Try looking at the jacobian, curvature, and/or gyrfication - Examine the individual VBM results carefully to make sure that they are not being driven by an outlier and that the segmentation looks ok. - Voets, 2008, NI did a comparison where they looked at some of these issues. doug Allison Stevens wrote: Fatima, I can't really say anything on this topic but I did want to point you to some information on FreeSurfer vs. VBM: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.WhataretheadvantagesofFreeSurferoverVBM.3F Allison On Fri, 8 Jul 2011, Ahmed, F, Me fah...@sun.ac.za 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] muliple fressurfer instance and cuda
2011/7/8 Knut J Bjuland knut...@hotmail.com: It work fine with just one GPU-assisted recon-all. Sorry, I messed up earlier, and didn't send my reply to the list. your experience makes sense, since the Freesurfer programs make no attempt to share the GPU beyond that which the driver imposes. Running out of memory (particularly on a low end card like yours) would not be surprising when running three recon-alls at once. Richard ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Optseq with Sparse Sampling
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 ___ Freesurfer mailing list Freesurfer@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.
