[no subject]

in (cached, score=-0.998, required 5, autolearn=disabled, HTML_MESSAGE 0.00, MAILING_LIST_MULTI -1.00, RP_8BIT 0.00) X-Spam-Status: No, No Subject: Re: [Freesurfer] temporal lobe errors in rh.white and lh.white surfaces but not in rh.orig and lh.orig surfaces X-BeenThere: freesurfer@nmr.mgh.har

[no subject]

EADER 0.00, HTML_MESSAGE 0.00, MAILING_LIST_MULTI -1.00, RP_8BIT 3.03) X-NMR-MGH-MailScanner-SpamScore: sss, ss X-Spam-Status: No, No Subject: [Freesurfer] Omitting aseg regions from segmentation X-BeenThere: freesurfer@nmr.mgh.harvard.edu X-Mailman-Version: 2.1.9 Precedence: list List-Id:

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core=1.124, required 5, autolearn=disabled, HTML_MESSAGE 0.00, RP_8BIT 1.12), not spam, SpamAssassin (cached, score=0.124, required 5, autolearn=disabled, HTML_MESSAGE 0.00, MAILING_LIST_MULTI -1.00, RP_8BIT 1.12) X-NMR-MGH-MailScanner-SpamScore: s X-Spam-Status: No, No S

[no subject]

x-uw-ex-currentlocation-365-recipient: Outside x-microsoft-antispam-prvs: x-exchange-antispam-report-test: UriScan:(35762410373642); x-ms-exchange-senderadcheck: 1 x-exchange-antispam-report-cfa-test: BCL:0; PCL:0; RULEID:(8211001083)(6040522)(2401047)(8121501046)(5005006)(10201501046)(3

[Freesurfer] (no subject)

Hello,everyone Your reply said I can't use alphasim with qdec.By the way ,Could I use alphasim in other ways in FreeSurfer,for example command line ? Best regards. Xin-Fa Shi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

[Freesurfer] (no subject)

hello, I have two question: 1- I use GNU-parallel to run recon-all on my computer. i have 50 or so subject but after processing around 10 subject i get this error: "rm no match found", and the process won't continue. it only give me this error one after another.do you know what is my problem? 2-

[Freesurfer] (no subject)

Hi, I am trying to run the tkmedit command ("tkmedit subject_name brainmask.mgz -aux T1.mgz") and keep getting the following error message: ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please s

[Freesurfer] (no subject)

Hello all, I have two question. 1- I am unable to read a surface to matlab, can you please give me an example. how should i load a surface with overlay to matlab and display it (e.g. do it for bert) 2- another question, can we use another test in place of t-test? how? WRG A.Faghiri _

[Freesurfer] (no subject)

Hello again, I forgot to ask one of my main questions: averaging subjects to fsaverage. if i run recon-all with -qcache all my subjects will be averaged to fsaverage subject, right? then will the fsaverage change after i do this, and if it change doesn't it affect my future projects? WRG A.Faghir

[Freesurfer] (no subject)

Hi, I am pretty new to the Freesurfer. I want to get the idea how the freesurfer differentiate 6 layers. I have already get the pial/ gray matter,gray/matt white matter, thickness map, then how to calculate and form the laminars? Thanks! -- Yun Wang _

[Freesurfer] (no subject)

Hi freesurfer experts, We are analyzing data from a simultaneous PET-MRI study, and are having problems overlaying BPnd volume files onto our subjects' volume space. I've attached an image of the issue-- it seems as if the BPnd image is shifted towards the left of the subject's brain. Our BPn

[Freesurfer] (no subject)

Could someone please tell me how to unsubscribe from this list? I couldn't find it on the website. Thanks On Jul 2, 2015 4:56 AM, "Milde, Christopher" < christopher.mi...@zi-mannheim.de> wrote: > Dear Freesurfers, > > I have problems converting .nii.gz files into .mgh files needed e.g. for > perf

[Freesurfer] (no subject)

Hello Freesurfers I meet a problem in calculate Lgi I run fs in vituralBOX, matlab is installed. At the begining everything seems fine .but error come in "make_outer_surface". The details are in below. = xubuntu-VirtualBox:~> recon-all -s test001 -loc

[Freesurfer] (no subject)

Hi FS, MR images of two of my subjects in a group have been acquired with different T1 protocol from the rest. All the subjects has been acquired with sagittal 1mm iso : Width: 230.00 mm (256) Height: 230.00 mm (256) Resolution: 1.113 pixels per mm Pixel size: 0.90x0.90 mm and these two with cor

[Freesurfer] (no subject)

Hello Freesurfer Experts, For a longitudinal dataset we worked on some time ago, in version 5.1, we want to add subjects with only one time point. According to the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing we can do this by passing only a single time poin

[Freesurfer] (no subject)

Hi, The recon pipeline outputed an apparently correct file, which happen to confuse freesurfer reading functions. I attached a slightly-altered file named lh.data_crash which have the same problem. The other file named lh.data_nocrash seems to be parsed fine, despite differing by only 1 float-

[Freesurfer] (no subject)

Thanks Doug, I already downloaded the new script for mri_label2vol, but it seems it is just compiled for linux, as I cannot execute it in my Mac. If it is so, could you please upload another compiled for mac, or source. Thanks Jose > For the missing insula problem, try using a newer version of

[Freesurfer] (no subject)

Dear Freesurfer Experts, Are the fsaverage files necessary for qdec analysis? Regards ___ 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 on

[Freesurfer] (no subject)

Hello, We are trying to figure out how to expand the pial surface after FreeSurfer processing has occured. The processed brainmask.mgz has defined the gray matter as red, but the pial surface does not extend out to the red gray matter on a portion of the temporal lobe. Is there a way to expand

[Freesurfer] (no subject)

Hi, I would like to "sculpt" a label according to Talairach coordinates, precisely to cut the anterior part of the rostral middle frontal gyrus after +50mm AP; how would you procede ? Thank you for your software and thank you in advance for your help ! Yours sincerely, Pj Le Reste __

[Freesurfer] (no subject)

Hi list, Where Can I find basic information about entorhinal cortex analysis? Thank you very much. Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

[Freesurfer] (no subject)

Hi FreeSurfer experts, I would need to use the registration tools in freesurfer because the fsl ones ga ve me some problem. Just to try I have run mri_ca_registration and mri_cvs_registration and so I hav e three questions: 1) mri_ca_registration generates a talairach tansform file in .m3z format

[Freesurfer] (no subject)

Hi FreeSurfer experts, I would need to use the registration tools in freesurfer because the fsl ones ga ve me some problem. Just to try I have run mri_ca_registration and mri_cvs_registration and so I hav e three questions: 1) mri_ca_registration generates a talairach tansform file in .m3z format

[Freesurfer] (no subject)

Has anyone ever ran a post contrast sequence in FreeSurfer? Thanks, Ashley -- * * ___ 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 f

[Freesurfer] (no subject)

Hello Freesurfer I would like to extract the stream for surface-based analysis on the output of an in-house segmentation process. Is this possible?How? Thanks Shani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard

[Freesurfer] (no subject)

Hello all I have created white matter surface of a non primate brain and I'm trying to use mris_make_surfaces to position the pial surface. The problem is that the resulted pial surface is miss-positioned-the 'growing' stops very close to the white surface (no gradient visible where it stops) Any

[Freesurfer] (no subject)

Hello, I am currently attempting to download the freesurfer software onto my mac device from the website, but I am having trouble. None of the links will open, and when I tried typing the wget (curl-O for me) command into my command line, nothing happened. Any suggestions? Thanks, David ___

[Freesurfer] (no subject)

with_focb_100_use_this_6_2.log Description: Binary data with_focb_100_use_this_6_2.sum Description: Binary data with_focb_100_use_this_6_2.xtxideal.mat Description: Binary data with_focb_100_use_this_6_2-001.par Description: Binary data ___ Frees

[Freesurfer] (no subject)

excuse me but i don't understand what you mean by "terminal of mri_label2volume" Thank you for help ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail i

[Freesurfer] (no subject)

Dear Freesurfer Users, I am trying to regress out the activity associated with button presses in my GLM analysis. How do I generate a nuisance regressor file analogous to a white matter regressor generated in functional connectivity (a one column time course file)? Thanks you, Nick _

[Freesurfer] (no subject)

Hi Dr. Fischl, I had a couple subjects that failed recon-all. Although the error log said recon-all failed at mri_watershed it looks like the root problem is a couple steps earlier, because the nu.mgz looks too dark. This was discussed in a previous thread from 2008. http://www.mail-archive.com/f

[Freesurfer] (no subject)

Hi Doug, I have run recon-all -s subject -cortparc -parcstats and the process finished without errors, but the aparc files do not have the perirhinal cortex on it. I have noticed that when I recon with 5.3 perirhinal labels are created on the label folder, but when I run recon-all -s subject -c

[Freesurfer] (no subject)

-- Dott.ssa Valentina Ciullo Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportamentale IRCCS Fondazione Santa Lucia via Ardeatina 306 - 00179 Roma Tel. +39(0)651501101 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com

[Freesurfer] (no subject)

Hi: Which is the optimal parameters for a morphometric sequence (fspgr?) n a 1.5 T MR OPTIMA 450w GE MRI equipment ?... Because, we are using an fspgr 1mm isotropic sequence, but we got wrong defined borders in some structures... for example, hypocampus, cortex-wm... I think it could be because th

[Freesurfer] (no subject)

Good morning Dr Vinke, did you have the chance to take a look at the subject I uploaded a few days ago? thanks again. Kind regards, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscie

[Freesurfer] (no subject)

hi guys i'm getting a 'Couldn't create output file .xdebug_tkmedit' before loading volumes, any suggestions on what I can do would be most welcome. Also got: ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable.

[Freesurfer] (no subject)

Hi freesurfer crew, I found some details through this website http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/surfstat/index.htm about cortical thickness maps with freesurfer. I have done some reading but can't really make much sense of how I might do this for a single subject thr

[Freesurfer] (no subject)

Hello, I noticed that Freesurfer's latest release offers an expert option "added -first_wm_peak flag to mris_make_surfaces, which may aid accurate more white matter surfaces especially in heavily myelinated areas like visual cortex on data that is higher res than 1mm. enable the flag via an expert

[Freesurfer] (no subject)

   Good afternoon;   I am hoping you can help me answer a pretty quick & easy question….   I am trying to identify the best MRI protocol to use for Freesurfer analysis… When I look at the FAQ:   Data Requirements   The processing procedures for the creation of cortical models require good quali

[Freesurfer] (no subject)

Hi guys, just wondering what you'd say is the best measure for whole brain volume? Cortex volume.. Cortical white matter volume.. Total gray volume.. Intracranial volume.. etc. Cheers! Hugh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] (no subject)

-- ___ 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

[Freesurfer] (no subject)

Dear freesurfers, This is the first time I am posting so hope the following makes sense, I don't use freesurfer but manage the installation of freesurfer on our cluster. We have a user who is trying run a script that submits a recon-all job to our cluster using the -localGI flag: recon-all -su

[Freesurfer] (no subject)

Hi FreeSurfer experts, I'm running a task-based analysis on mni305 space, running a regression of load-dependent activation on RBC folate values, regressing out the effects of age and gender. The analysis runs fine, but when I visualize the sig.mgh map in tkmedit there is a border of functiona

[Freesurfer] (no subject)

Hello, I made an analysis thanks to the QDEC tool : I tested a correlation between an inhibition score and cortical thickness, corrected for age (continuous = inhibition score ; nuisance = age ; smoothing = 25 and FDR corrected) *** * ** *** * *** *** *** ** ***

[Freesurfer] (no subject)

Hi Doug et al, I would like to get a different cluster summary stat out of mri_glmfit-sim. Rather than size, I'd like to use the "sum of t-scores" (after Maris & Oostenwald 2007, for example). That is, set a cluster inclusion threshold, and then for each cluster of adjacent vertices that clear the

[Freesurfer] (no subject)

Hi I am using freesurfer for calculation cortical thickness in my subjects. Firstly, I have converted all the T1 weighted images from dcm into nii.gz format. After that, I have run the recon-all in one subject using this script 'recon-all -i CON_101.nii -s CON_101 -all' , but it shows error The

[Freesurfer] (no subject)

Hello FreeSurfer Developers, I'm running the recon-all on my subjects data as described in freesurfer tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial), but it shows the following error when I run the recon-all command: ERROR: cannot find CON_101.nii recon-all -s exited with ERRO

[Freesurfer] (no subject)

Hello FreeSurfer Developers, I'm running the recon-all on my subjects data as described in freesurfer tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial), but it shows the following error when I run the recon-all command: ERROR: cannot find CON_101.nii recon-all -s exited with ERRO

[Freesurfer] (no subject)

Hello FreeSurfer Developers, I’m attempting to make some performances evaluation on recon-all using GPUs on a node with 4 nVidia K80. Submitting different instances of recon-all on 8 different subjects, every instance run on the same device (#0), compromising the efficiency of the test. Is there a

[Freesurfer] (no subject)

Hello: I am using QATool in Freesurfer, and the script requires FS 5.1 and also works for 5.3 which i am using, but when i run it, it always gives me error about license: ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. But FS 5.3 works fine with the license file lic

[Freesurfer] (no subject)

Dear Dr. Iglesias, Using the originally released version 6 (the one that was "unreleased") I ran the recon -all -all and the subfield segmentations on a sample. I noticed that the program was taken down then put back online after some updates. Do you recommend we re-run these segmentations with

[Freesurfer] (no subject)

Dear all, I am very new to using TRACULA and Freesurfer. I am trying to apply tracula on the provided tutorial data. When I ran the command trac-all -prep -c dmrirc.tutorial, after eddy current correction, I get this error: -- D. ___ Freesurfer mailing

[Freesurfer] (no subject)

-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informatio

[Freesurfer] (no subject)

Hello, I recently downloaded freesurfer on my mac with a Yosemite operating system. The application itself appears to work, however I am not able to use the command line to do any of the testing free surfer commands, as I keep getting a access denied. I have attached a screenshot. Your help would

[Freesurfer] (no subject)

Hi all, I'm testing Freesurfer 5.3 and have a question about processing 1.5T versus 3.0T scans. Specifically, is there a switch in recon-all? I've observed some using a "-3T" switch, but I can't see this option documented in the "recon-all -help" output. I've executed test runs on a VM both with

[Freesurfer] (no subject)

I just want to run plane correlation with the csf-variable best Eric ___ 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

[Freesurfer] (no subject)

I just want to investigate significant correlation with the csf variable correcting for apoe-status, gender, diagnosis and age below previous correspondence your classes are right. What are you trying to test with your contrast matrix? On 01/20/2016 05:33 AM, Erik Lindberg wrote: > Dear Freesur

[Freesurfer] (no subject)

Hello!  My name is Achcha. I am a PhD student of Russian Medical Academy for Postgraduate Education. In my research "Dementia with Lewy bodies" (DLB) I am going to determine the association between the focal atrophy measures on MRI and to compare it with clinical features of DLB. I try to inst

[Freesurfer] (no subject)

Hi,I'm wondering whether the FS-FAST performed bandpass filtering. Stefano ___ 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 pe

[Freesurfer] (no subject)

Hi, I’m new to freesurfer, I’m an undergraduate currently doing research involving analyzing mri scans to produce volume measurements of the hippocampus. I’ve been using FSL’s FIRST method to do this thus far, but from what I’ve read online, freesurfer is much better for volumetric analysis of

[Freesurfer] (no subject)

Dear all, I need to compute the geodesic distance (i.,e. the distance on the cortical surface) between a series of vertices. Specifically, I want to compute the distance between all the vertices in the right hemisphere (>10) and a series of vertices of interest (around 2), always located

[Freesurfer] (no subject)

Dear experts, I would like to ask you for some advice about matrix. I use FreeSurfer for automatic segmentation of infant brains and have a problem with infants under 6 months. Could you give me advice what are the optimal parameters of the matrix for automatic segmentation from newborns to 6-month

[Freesurfer] (no subject)

Dear experts, I would like to ask you for some advice about matrix. I use FreeSurfer for automatic segmentation of infant brains and have a problem with infants under 6 months. Could you give me advice what are the optimal parameters of the matrix for automatic segmentation from newborns to 6-month

[Freesurfer] (no subject)

Hello, As we know, Freesurfer generates separate surface models and associated labels for each brain hemisphere, is there any way to merge two hemisphere and come up with a single cortex surface? My best, Saeed ___ Freesurfer mailing list Freesurfer@nmr

[Freesurfer] (no subject)

Hi Doug et al, We have been working on a linear regression-type analysis (see attached analysis.info for analysis and slopepar for a sample paradigm file) that involves task-related activation in a working memory test. For each participant, there are four conditions: 1, 3, 5, and 7 items that nee

[Freesurfer] (no subject)

Hi everyone, I'm using optseq2 to optimize a fmri design. Whenever I try to add the --tnullmin parameter I end up with either a segmentation fault or a glibc error (see examples). May someone explain me what is going wrong? Thanks! Regards, Jacob Info: optseq2 2.14 linux 64-bit and 32-bit Examp

[Freesurfer] (no subject)

Hi, I am trying to use selxavg3-sess function and getting this error. Below is the error I get. I actually have this fingertap.par file but freesurfer somehow does not see it. Any help would be appreciated. Thanks! Meryem Yucel PMI Lab Extension format = nii.gz ERROR: opening /autofs/space/m

[Freesurfer] (no subject)

Hi, I have few questions and I will appreciate if anyone can help: 1) Can I get more clusters after I correct for multiple comparison than the number of clusters I have in the uncorrected results? Is this possible? 2)When I change the smoothing from fwhm 10 to fwhm 20 for example why I a

[Freesurfer] (no subject)

Hello all, I'm encountering a problem when I try to compare two timepoints for a particular subject. I run the command "recon-all -all -s 7107-46-tp1 -i 7107-46-1/001.mgz" and the end of the output stream where I receive errors shows the following below. Any help is greatly appreciated! paintin

[Freesurfer] (no subject)

Dear FS experts, I would like to know if for a Diffusion tensor imaging (DTI) tractography study with TRACULA I can use my previous results from FSTutorial/Diffusion more exactly my results after running dt_recon and registrations on the CVS space. If not can you please advise me if for a DTI prob

[Freesurfer] (no subject)

Dear Freesufer experts, I am wondering if it is possible to tell mri_vol2surf to ignore certain voxels in the src volume, for instance, by setting their intensity to -999. I'm trying to project only gray matter voxels from a PET scan onto the fsaverage surface, but when I use an only-GM PET image

[Freesurfer] (no subject)

Hello Freesurfer experts, How can I specify multiple contrasts for my thickness study with two groups AA and BB, having different number of subjects in each group? My variables are tract-wise FA values, age and IQ. Thanks in advance, Shantanu -- Shantanu Ghosh, Ph.D. Martinos Center for Biome

[Freesurfer] (no subject)

Freesurfers A real real general question here: if i am running a glm_fit for cortical thickness with a fsgd with 2 groups (G1, G2) and 3 continues variables and have a matrix of 1 -1 0 0 0, red/yellow areas mean that G1 is thicker in this area than G2, correct? Best- Michael -- Michael D. Kr

[Freesurfer] (no subject)

Please, could anyone let me know how to perform statistical analysis in QDEC to look at the interaction between two genes on cortical thickness?    Vincenzo Pierro ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.

[Freesurfer] (no subject)

Hi, So when using command tkmedit *subjID* brainmask.mgz -aux -wm.mgz -surfs I receive the message: "Error: Parsing -aux option Expected an argument This option needs an argument: the image type, directory, or file name of the data to load as the aux volume." My apologies if there is an obvious

[Freesurfer] (no subject)

Hello, I'm conducting a longitudinal analysis and encounter an error when running the "long_mris_slopes" command (this is contained in the online tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial). The error that arises within a minute is "ERROR -10 : mris_calc

[Freesurfer] (no subject)

Hi, How can I get sulcal depth measurements from Freesurfer? Cheers, Hugh ___ 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 p

[Freesurfer] (no subject)

Dear FreeSurfer expects, I ran a cortical thickness analysis that revealed many significant clusters, but half of them are pretty small. Is there a possibility in qdec to display only clusters with a certain clustersize on the inflated surface? Thank you very much for your help, best wishes, Mar

[Freesurfer] (no subject)

Hello all, I'm analyzing the data for a training study our research group conducted, and I'm looking to see if there are changes in cortical thickness as a result of training. We have pre- and post-training scans, so I followed the longitudinal tutorial ( http://surfer.nmr.mgh.harvard.edu/fswiki

[Freesurfer] (no subject)

Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/subjects/B__/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces w

[Freesurfer] (no subject)

Dear all, I am carefully starting up with the basics for analysis of 3T mri images. After having done the recon all I am about to begin the review and editting process where needed. However, I am now a bit overwhelmed. Is there any logical or recommended order to proceed with the several potential

[Freesurfer] (no subject)

96 Normal 0 false false false EN-US X-NONE X-NONE

[Freesurfer] (no subject)

Bruce, I tried mris_fill, but it gives me a filled white matter volume (I already have that in the mri directory. I need the contour only. Douglas, Looking into the --help gave me a few ideas. I think the help page (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol ) should include this infor

[Freesurfer] (no subject)

Hi all, I'm trying to figure out a way to do create seed-based structural covariance networks through Freesurfer like the one shown in the link below. From the images, it looks like it's done through QDEC. Any tips how to get started? https://ww5.aievolution.com/hbm1601/index.cfm?do=abs.viewAbs

[Freesurfer] (no subject)

Apologies-- This email contains attachment. Thank you. Hello, I am trying to implement using Freesurfer segmentation in my analysis for MEG data. I am trying to segment this structural MRI (1400composite.dcm) and I keep getting errors. I hav

[Freesurfer] (no subject)

Hello, I try to map the surface to the native space, using the following command adjusted for my data: mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --hemi lh --s subjectname the output is: ERROR: --tval-xyz flag needs 1 argument FYI: --tval-x

[Freesurfer] (no subject)

Hi all, I have finished the command “recon -all” without error. But I get an error that says: “Received X error! Error code :158 Request code : 148 Minor code: 2 Error text :’GLXBadLargeRequest’” I am using the command “tksurfer sub lh inflated”. Then clic

[Freesurfer] (no subject)

Dear Freesurfer, Is it possible to keep on the supporting list but without receiving emails from other people? My email account is getting stuck with so many emails. Thanks, Jose ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n

[Freesurfer] (no subject)

Respected Sir, How can i scoop out or separate only hippocampus from a 3D MRI of whole brain? With regards vidhu agarwal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The infor

[Freesurfer] (no subject)

Dear Freesurfer experts, I'm new to freesurfer and I'm now trying to get anatomical labels from the Destrieux Atlas. I know that we can easily extract labels using the tksurfer GUI by a couple of mouse clicks (load atlas -- click on one label -- save selected label), but I'm just wondering if ther

[Freesurfer] (no subject)

Hi Chris, If you could get support for CUDA 5.5 it would be marvelous. I'm quite inexperienced with the CUDA programming (consider me an enduser), you would have my full support. I also have a computer here to do any testing if needed. I have a PC with CentOS 6.5, Freesurfer 5.3.0, i7 4770k, 1

[Freesurfer] (no subject)

Hi everyone, I'm getting the follow error and it's jus started happening after updating Xquartz.. any ideas what I can do? Also, i dont have a .debug_tkmedit file, when tkmedit was running normally the first line would say could not create debug file. Many thanks, Hugh ERROR: A segfault has occur

[Freesurfer] (no subject)

Dear FS experts, ___ 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

[Freesurfer] (no subject)

Dear all, I used the the 3 steps of longitudinal analysis explained in freesurfer longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each of time points. Is this equivalent to compute the (total gray matter volume + total cortical matter volume)/CSF from aseg.stats file ? Tha

[Freesurfer] (no subject)

Dear Freesurfers, I would interest about when will the freesurfer course takes place in 2015? I realy need this info due to a travel grant deadline. Thanks, Szilvia Nagy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.h

[Freesurfer] (no subject)

External Email - Use Caution Dear freesurfer experts, I want to calculate functional connectivity between two seeds with freesurfer-linux-centos6_x86_64_stable_pub-v6 . after using fcseed-config and fseed-sess commands, I use fcseedcor command. the command that I trying to run i

[Freesurfer] (no subject)

External Email - Use Caution Can? you send the full terminal output? On 12/05/2018 01:25 AM, Sara Jafakesh wrote: > > External Email - Use Caution > > > > > > > Dear freesurfer experts, > I want to calculate corrolation between two seeds with > free

[Freesurfer] (no subject)

External Email - Use Caution Hi everybody, after finishing my group analysis I am currently trying to run a ROI analysis. However I have some problems/general questions. I am trying to draw a ROI on fsaverage in order to use the mri_label2label command afterwards. I opened Freev

[Freesurfer] (no subject)

External Email - Use Caution Here is the message displayed: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/sub

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