[Freesurfer] missing tutorial data for Longitudinal Processing - Tutorial
Hi I am trying to follow the Longitudinal Processing - Tutorial but it appear that the tutorial data is missing at the server? Has the file been rename or moved to another place? Knut J Bjuland ___ 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] Question about volumetric group analysis
Hello, I have two questions about volumetric analysis: First: Are the volume measures in the files aseg.stats or ?h.aparc.stats (Gray Matter Volume) already normalized by ICV? Or should I divide all the structure volumes which I want to compare between subjects by the ICV of each subject? Second: When comparing gray matter volumes the correct is use the ICV or the total cortical gray matter volume to normalize? And if I have to use the total cortical gray matter volume, how can I obtain it? I know that this information is in the aseg.stats file, but I was wondering if I can use asegstats2table to extract it. Thank you very much, Fernanda ___ 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] Question about volumetric group analysis
Hi, Nothing in the stats is normalized. It makes sense to normalize volumes by ICV when comparing across subjects (as that is assumed to stay constant while GM volume of course changes ). Not sure if aseg...table grabs it, it should, maybe Krish knows. Best Martin On May 17, 2011, at 8:19 AM, Fernanda Palhano wrote: > Hello, > > I have two questions about volumetric analysis: > First: Are the volume measures in the files aseg.stats or ?h.aparc.stats > (Gray Matter Volume) already normalized by ICV? Or should I divide > all the structure volumes which I want to compare between subjects by the ICV > of each subject? > Second: When comparing gray matter volumes the correct is use the ICV or the > total cortical gray matter volume to normalize? And if I have > to use the total cortical gray matter volume, how can I obtain it? I know > that this information is in the aseg.stats file, but I was wondering if I can > use asegstats2table to extract it. > > > Thank you very much, > > Fernanda > > ___ > 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.
Re: [Freesurfer] missing tutorial data for Longitudinal Processing - Tutorial
Yes, the data is currently missing as we have to rerun all tutorials with the new FS version 5.1 before release. Will be up again in a week . Best Martin On May 17, 2011, at 5:32 AM, Knut J Bjuland wrote: > Hi > > I am trying to follow the Longitudinal Processing - Tutorial but it > appear that the tutorial data is missing at the server? Has the file > been rename or moved to another place? > > > Knut J Bjuland > ___ > 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.
Re: [Freesurfer] Question about volumetric group analysis
Hi Fernanda, The choice between ICV vs a measure of total "brain volume" or total cortical gray matter volume depends on whether you want to control for potential overall brain atrophy. Using ICV will control for overall "head size", but not for potential overall brain atrophy (e.g., with age, or related to dementia). Using total cortical gray matter will control for overall brain atrophy and thus would allow you to say that changes in a given structure were "above and beyond" any existing global atrophy. Personally, I find it more informative to control for potential global atrophy, and thus use total cortical gray matter rather than ICV. After all, if a structure is decreased in size, but the overall brain is decreased as well, you have not established anything regarding the specificity of that change to the structure of interest if you use ICV as the covariate. cheers, -MH On Tue, 2011-05-17 at 09:19 -0300, Fernanda Palhano wrote: > Hello, > > I have two questions about volumetric analysis: > First: Are the volume measures in the files aseg.stats or ? > h.aparc.stats (Gray Matter Volume) already normalized by ICV? Or > should I divide > all the structure volumes which I want to compare between subjects by > the ICV of each subject? > Second: When comparing gray matter volumes the correct is use the ICV > or the total cortical gray matter volume to normalize? And if I have > to use the total cortical gray matter volume, how can I obtain it? I > know that this information is in the aseg.stats file, but I was > wondering if I can use asegstats2table to extract it. > > > Thank you very much, > > Fernanda > > ___ > 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] Segmentation Fault
Not happening anymore, thanks! > Hi Chinduri, is this still happening? I can't replicate. > > doug > > Chindhuri Selvadurai wrote: >> Hi all, >> >> We are trying to run individual analyses on several subjects, and we >> keep >> getting a 'Segmentation Fault.' We have run other subjects with the >> same >> command a while ago, and the command worked fine at that time. Do you >> have any idea what would be causing this error? The output is included >> below: >> >> Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15 >> Subjects Dir: /cluster/manoach/milton/subjects >> FreeSurfer v. Stable 5 >> >> >> Session: /autofs/cluster/manoach/milton/subjects/PBMCT15 >> >> Fri May 13 12:21:58 EDT 2011 >> Run: 012 >> Fri May 13 12:21:58 EDT 2011 >> Update not needed >> Fri May 13 12:21:58 EDT 2011 >> register-sess completed >> PBMCT15 MC - >> mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d >> /autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run >> -nolog -update >> Logfile is /dev/null >> --- >> /autofs/cluster/manoach/milton/subjects/PBMCT15 >> RunList: 012 >> --- ** --- >> --- Motion Correcting Run 012 --- >> --- ** --- >> sess = PBMCT15 >> Fri May 13 12:21:58 EDT 2011 >> mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat >> 012/fmcpr.mcdat >> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold >> mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii >> log file is 012/fmcpr.nii.gz.mclog >> mcdat file is 012/fmcpr.mcdat >> tmp dir is 012/tmp.mc-afni2.3377 >> #@# >> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold >> mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz >> --nskip >> 0 --ndrop 0 -odt float >> mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz >> --nskip >> 0 --ndrop 0 -odt float >> nskip = 0 >> ndrop = 0 >> $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ >> reading from 012/template.nii... >> TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-0.998297, -0.0395807, 0.0428535) >> j_ras = (0.0411249, -0.998513, 0.0357732) >> k_ras = (0.0413739, 0.0374746, 0.998441) >> changing data type from short to float (noscale = 0)... >> writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz... >> #@# >> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold >> mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float >> mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float >> Segmentation fault >> >> >> Thanks! >> >> Best, >> >> Chindhuri Selvadurai >> >> Psychiatric Neuroimaging, Manoach Lab >> Martinos Center for Biomedical Imaging, MGH >> Phone: (617)726-0307 >> ___ >> 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 > > > Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ 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] different V1 sizes for same subject in two different sessions
Hello All, I have estimated V1 using Hinds and Fischl method for some subjects scanned on two different days. I've been going through the V1 surface area data for these. One thing that concerns me is that is seems that very different V1 sizes are reported for the same subject when scanned on different dates and each run through the cross sectional stream. I am trying to check the test-re-test values for these. Any idea why this is so and whats a better method to do the comparison ? Thanks Ri ___ 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] Question about volumetric group analysis
Fernanda Palhano wrote: > Hello, > > I have two questions about volumetric analysis: > First: Are the volume measures in the files aseg.stats or > ?h.aparc.stats (Gray Matter Volume) already normalized by ICV? Or > should I divide > all the structure volumes which I want to compare between subjects by > the ICV of each subject? You will need to do the normalization yourself. > Second: When comparing gray matter volumes the correct is use the ICV > or the total cortical gray matter volume to normalize? And if I have > to use the total cortical gray matter volume, how can I obtain it? I > know that this information is in the aseg.stats file, but I was > wondering if I can use asegstats2table to extract it. Whether you should use ICV or GM volume is a matter of debate that depends on exactly what you are trying to do and what structure you are studying. Your hypothesis that you are testing should have a statement about normalization. The ICV and total GM volume automatically show up as a column when you run asegstats2table. doug > > > Thank you very much, > > Fernanda > > > > ___ > 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] Question about volumetric group analysis
For subcortical structures, you could consider using a covariate measure that itself includes subcortical gray matter. Not sure if the latest FS version has such a measure automatically constructed or not. In the past, we have used "whole brain volume" as a covariate for analysis of both cortical and subcortical structures, with "whole brain volume" defined as the volume contained within the pial surface (obtained using mris_volume) minus the volume of the lateral ventricles (contained within the aseg). cheers, -MH On Tue, 2011-05-17 at 10:19 -0300, Fernanda Palhano wrote: > Thanks, Michael. > > I have a follow up question. > If I understood, I should use the total cortical gray matter volume to > control for a global change > in cortical brain volume, so for exemple, if I'm interested in the > volume of parahippocampal gyrus, > I can normalize this way. And, once I have the measures for both the > hemispheres separately, I have to use the total cortical gray matter > of each one > to normalize? > But for other structures like hippocampus or amigdala it makes sense > to control using volume of gray matter? Or, I continue using the ICV? > > Thanks again, > > > On Tue, May 17, 2011 at 9:57 AM, Michael Harms > wrote: > > Hi Fernanda, > The choice between ICV vs a measure of total "brain volume" or > total > cortical gray matter volume depends on whether you want to > control for > potential overall brain atrophy. Using ICV will control for > overall > "head size", but not for potential overall brain atrophy > (e.g., with > age, or related to dementia). Using total cortical gray > matter will > control for overall brain atrophy and thus would allow you to > say that > changes in a given structure were "above and beyond" any > existing global > atrophy. > > Personally, I find it more informative to control for > potential global > atrophy, and thus use total cortical gray matter rather than > ICV. After > all, if a structure is decreased in size, but the overall > brain is > decreased as well, you have not established anything regarding > the > specificity of that change to the structure of interest if you > use ICV > as the covariate. > > cheers, > -MH > > > On Tue, 2011-05-17 at 09:19 -0300, Fernanda Palhano wrote: > > Hello, > > > > I have two questions about volumetric analysis: > > First: Are the volume measures in the files aseg.stats or ? > > h.aparc.stats (Gray Matter Volume) already normalized by > ICV? Or > > should I divide > > all the structure volumes which I want to compare between > subjects by > > the ICV of each subject? > > Second: When comparing gray matter volumes the correct is > use the ICV > > or the total cortical gray matter volume to normalize? And > if I have > > to use the total cortical gray matter volume, how can I > obtain it? I > > know that this information is in the aseg.stats file, but I > was > > wondering if I can use asegstats2table to extract it. > > > > > > Thank you very much, > > > > Fernanda > > > > > ___ > > 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] different V1 sizes for same subject in two different sessions
No, that sounds like something went wrong. How does the calcarine label look in the parcellation? On Tue, 17 May 2011, Ritobrato Datta wrote: > Hello All, > > I have estimated V1 using Hinds and Fischl method for some subjects scanned > on two different days. I've been going through the V1 surface area data for > these. One thing that concerns me is that is seems that very different V1 > sizes are reported for the same subject when scanned on different dates and > each run through the cross sectional stream. > I am trying to check the test-re-test values for these. > > Any idea why this is so and whats a better method to do the comparison ? > > Thanks > > Ri > > > ___ > 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 Average Subject
Dear Dr. Fischl, We have been following the steps you have laid out on the listserv (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17601.html) to make an average subject. However, we are not able to proceed with the mris_preproc step. It requires an output file and the hemisphere. When we include these, it asks for an input file. The command we are inputting is: mris_preproc --surfreg sphere.reg.avgsubject --s nc_001 --s ... and mris_preproc --surfreg sphere.reg.avgsubject --hemi rh --s nc_001 --out avgsubject.mgz Could you please advise us on how to proceed? Thank you. Regards, Massieh Moayedi ___ 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] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
mri_convert -iks 1 --conform ga_2010.nii 001.mgz will create an image where the z direction is 1mm. but the orientation will still be wrong, since it was missing from the header (or incorrect). orient_mri can be used to rotate it, but one cannot know whether left or right is correct. n. On Mon, 2011-05-16 at 21:35 -0300, Pedro Paulo de Magalhães Oliveira Junior wrote: > The images are: 0.5 x 0.5 x 1.0 > > > Can mri_convert fix it or should I edit the Nifti header? > > 2011/5/16 Nick Schmansky > PPJ, > > Hi, > > mri_info /space/incoming/ga_2010.nii > > shows that the image is 0.5 x 0.5 x 0.5. but when viewing in > freeview > or tkmedit, the brain seems 'squashed', as if there is a slice > gap. do > you know the details of how this was acquired? > > N. > > > > On Mon, 2011-05-16 at 17:49 -0300, Pedro Paulo de Magalhães > Oliveira > > Junior wrote: > > I'm having this error in the recon-all > > > > > > # > > #@# Talairach Mon May 16 16:38:01 EDT 2011 > > /usr/local/freesurfer/subjects/GAGRICOLA/mri > > > > > > talairach_avi --i orig.mgz --xfm > transforms/talairach.auto.xfm > > > > > > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log > > > > > > I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the > > talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the > original > > nifti image as ga_2010.nii > > > > > > Any hints? > > > > > > > > > > > ___ > > 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] No inflated brain...
Hi Bruce, returning back to this. I tried the same command on the tutorial data set (bert): tksurfer bert rh inflated and I did not get the error about rh.sphere.reg surface not matching rh.inflated that I got with my data, but I still have the same problem with the tutorial data (bert). I see only a tiny part of the inflated brain in tksurfer. I have not tried to use tksurfer except to look at the inflated brain (my data then bert). For example if we were looking at an egg, I would only see one little piece of the shell, maybe 10% of the whole shell. Not sure what to do next. Since this happens with the tutorial data, I'll give you the info you indicated: Graphics card: Dell WH242 Nvidia Quadro FX 3500, 256MB, Dual DVI Out, PCIe x16, MRGA13 CRD,GRPHC,256,FX, OS: Running Red Hat Enterprise 5, which auto updates so I would think I have the latest drivers I access this machine remotely using NX from a Dell Precision T5500 running Win7 64. Here are the rest of the machine specs in case they are helpful (except have upgraded to red hat 5): 1DJ301Kit, Mouse, Universal Serial Bus, 2BTN, Optical, Lead Free Black1MX961Assembly, Card, PERC5I-ADAPTER Serial Attached SCSI1PD147Assembly, Cable, Light Emitting Diode, Hard Drive, Auxiliary Precision Workstation, 4901PJ058Assembly, Cable, Interface Serial Attached Scsi, Hard Drive, 4, Precision Workstation1 DC740KIT..., SOFTWARE..., RED HAT ENTERPRISE LINUX..., 4WS, PRECISION WORKSTATION..., SUBSCRIPTION..., 1YR, W1JK141KIT..., SOFTWARE..., RED HAT ENTERPRISE LINUX..., 4WS, INTEL EXTENDED MEMORY 64 BIT TECHNOLOGY..., MEDIA...1RP434Assembly, Floppy Drive 1.44MEGB, Nec Corporation, 05 Black16 GM431Dual In-line Memory Module, 2G 667M, 256X72, 8, 240, 2RX41MH366INSTRUCTION..., DEVIATE CHAS L6 TO L5+1XM459Processor, 80563K, Xeon Clovertown, X5355, LGA771, Burn34UF070Connector, Serial Attached Scsi, 22P, S, G, INTERPOSER0 149DFINFORMATION..., PREPARATION MATERIAL..., DEVIATION..., PRECISION WORKSTATION..., INCREASE..., #212R328Cord, Power, 15A, 125V, 5-15/C191YN124Assembly, DVD+/-RW..., 16X, IDE Hitachi LG Data Storage, Black1WH242Card, Graphics, 256, Fix, 3500 MRGA131TH836Keyboard, 104, UNITED STATES..., MULTI-MEDIA..., Black, LOGITECH...1XM459Processor, 80563K, Xeon Clovertown, X5355, LGA771, Burn31M8034Hard Drive, 146G, Serial Attached Scsi, 3, 15K, 3.5, FJT AL9L3 M8034Hard Drive, 146G, Serial Attached Scsi, 3, 15K, 3.5, FJT AL9L2WG404Assembly, Cable, Serial Ata, HardDrive, Precision Workstation Dozer -- Cell: 575-571-8274 Email: jkk...@gmail.com On Wed, Apr 27, 2011 at 5:38 PM, Bruce Fischl wrote: > so tksurfer has never worked for you on any dataset? Have you tried it on > one of the ones that we distribute? If it hasn't worked, we'll need to know > about your environment (what OS, what video card, are you running in a > virtual box, etc...) > > cheers > Bruce > > > On Wed, 27 Apr 2011, jim kroger wrote: > > No, I don't see anything, just black. >> Thanks, >> Jim >> >> >> >> -- >> Cell: 575-571-8274 >> Email: jkk...@gmail.com >> >> >> >> >> >> On Wed, Apr 27, 2011 at 4:52 PM, Bruce Fischl > >wrote: >> >> and do you see a hemisphere properly rendered or not? >>> >>> >>> On Wed, 27 Apr 2011, jim kroger wrote: >>> >>> Hi Bruce, this is my first attempt to see something in tksurfer. It's a >>> step in the making edits to white matter. I will go through the tksurfer tutorial, but I noticed that when I start tksurfer, there may be an error. Here's the output, think this might be it? (I am using red hat on a 32 gig Ram pretty fast machine, the drivers should be updated regularly along with all other updates) tksurfer heinrick rh inflated subject is heinrick hemiis rh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects Reading image info (/usr/local/freesurfer/subjects//heinrick) Reading /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz surfer: vertices=159373, faces=318742 mrisReadTriangleFile(/usr/local/freesurfer/subjects//heinrick/surf/rh.sphere.reg): surface doesn't match /usr/local/freesurfer/subjects//heinrick/surf/rh.inflated mrisReadTriangleFile failed. surfer: single buffered window surfer: tkoInitWindow(heinrick) surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... -- >
Re: [Freesurfer] MRI Signal Dropout
Hello, I have uploaded a subject via Martinos Center File Drop website. Have you had a chance to take a look? Thank you, Victor Yee On Wed, May 11, 2011 at 9:53 AM, Bruce Fischl wrote: > sure, upload a subject and we'll take a look > > On Wed, 11 May 2011, Victor Yee wrote: > > Hello, >> >> We have some signal dropout at the top of the brain in some scans, >> possibly >> similar to Rutvik Desai's 02/18/10 post. However, in our case, FreeSurfer >> is >> not including any of the regions affected by the dropout in both its >> subcortical segmentation and cortical parcellation. Instead, FreeSurfer >> essentially begins to treat the gray/white boundary as the CSF/gray >> surface, >> and classifies white matter as gray matter. The severity of this issue >> seems >> to correlate with how severe the dropout is. >> >> I have tried running nu_correct (normalization) for up to 256 iterations. >> This produces a noticeable effect when visualizing the volumes in tkmedit, >> but has no effect on FreeSurfer's output. I can upload a sample subject, >> if >> desired. We are using FreeSurfer 5.0 x64 on a Sun Grid Engine operating >> servers running CentOS 4.5. >> >> >> Thank you, >> Victor Yee >> >> > > 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] CORRELATION VALUE
Hi all, My design is very simple: 1-group,1-variable 2-nuisance (age,gender). I just want to see the correlation between Cth and my variable. I obtain one cluster after mc-correction. (using freesurfer5) There is any way to get the intercept,slope or r-pearson (in average) values of this particular cluster. What I've done is transform this cluster in a label to then visually inspect the Graph Average ROI, but I want the numerical results. Thanks in advance for your useful help. Cleo. ___ 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] Making a custom experimental template
Hi doug, I read your instructions on how to make an average subject, it looks quite streamlined. But I still have two questions about the procedure. 1. During the processing, every subject's surface need to register to a common target, and where the target comes from, it is an existed template in FreeSurfer or randomly selected from the pool of subjects, or something else? 2. In order to get a well-established or accurate average template, how many times does the function make_average_subject need to run? Thanks in advance, Lijie Huang On Tue, May 10, 2011 at 3:28 AM, Douglas N Greve wrote: > Hi Joakim, > > here are some instructions on what to do (some of which you've already > done): > > doug > > # Create an average subject (Creates $SUBJECTS_DIR/newtemplate) > make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ... > > # Register each subject to the new template (do for both lh and rh) > # Creates lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate > foreach subject (subj1 subj2 subj3 ...) > cd $SUBJECTS_DIR/subject > mris_register -curv surf/lh.sphere \ > $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \ > surf/lh.sphere.reg.newtemplate > end > > # Get thickness values in the newtemplate space for GLM analysis > mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s > subj3 ... > > # Create another average template based on the previous one: > # (Creates $SUBJECTS_DIR/newnewtemplate) > make_average_subject --out newnewtemplate --surf-reg > sphere.reg.newtemplate \ > --subjects subj1 subj2 subj3 ... > > > > > Joakim Vinberg wrote: > > Doug, > > Thanks! I just took a look at make_average_subject, and that looks > > quite a bit more streamlined--I think I'll just do that. > > Looking at make_average_subject, this should make the replacement for > > fsaverage. Following that, I would want to run mri_surf2surf to > > generate all of the surfaces in our new template space? > > Thanks! > > Joakim > > > > > > *From:* Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > > *Sent:* Fri 5/6/2011 9:46 AM > > *To:* Joakim Vinberg > > *Cc:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] Making a custom experimental template > > > > You are correct. If you run make_average_subject, it will create the > > template for you (as well as all the other files in a typical subject > > dir -- you'll need these to do a simple replacement for fsaverage). > > > > doug > > > > Joakim Vinberg wrote: > > > > > > Hi FS crowd, > > > > > > I just want to make sure that I have the process correctly described > > > for setting up a custom experimental template. I am basing this off of > > > the SurfaceRegAndTemplates > > > (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates), and > > > a hypothetical experiment with 10 subjects (s1, s2, …s10). I apologize > > > if this has been well-covered—I couldn’t quite match it on the website > > > or the archives. > > > > > > For the prep step, I believe my commands would be: > > > > > > mris_make_template lh sphere s1 custom_template_lh_0.tif > > > > > > mris_make_template rh sphere s1 custom_template_rh_0.tif > > > > > > which would result in two new template files names > > > custom_template_lh_0.tif and custom_template_rh_0.tif > > > > > > For Round 1, I would first create another registration for each > subject: > > > > > > mris_register s1/surf/lh.sphere custom_template_lh_0.tif > > > s1/surf/lh.sphere.regcustom_0 > > > > > > mris_register s1/surf/rh.sphere custom_template_rh_0.tif > > > s1/surf/rh.sphere.regcustom_0 > > > > > > … > > > > > > mris_register s10/surf/lh.sphere custom_template_lh_0.tif > > > s10/surf/lh.sphere.regcustom_0 > > > > > > mris_register s10/surf/rh.sphere custom_template_rh_0.tif > > > s10/surf/rh.sphere.regcustom_0 > > > > > > And then create another custom template: > > > > > > mris_make_template lh sphere s1 s2 s3 … s10 custom_template_lh_1.tif > > > > > > mris_make_template rh sphere s1 s2 s3 … s10 custom_template_rh_1.tif > > > > > > For round 2, I would repeat Round 1, generating a new set of > > > sphere.reg files, and then a new template, except substitute the > > > custom template from round 1 (custom_template_lh_1.tif and > > > custom_template_rh_1.tif). > > > > > > Then, I would register all of my data to the custom_template_lh_2.tif > > > and custom_template_rh_2.tif generated at the end of round 2. From > > > there, I am assuming that I could be able to use this new template as > > > I would fsaverage. Am I correct, or have I missed a step? > > > > > > Thanks in advance for all of your help! > > > > > > Joakim > > > > > > > > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve,
