[Freesurfer] ERROR: cannot find -cw256
Hello All, I am geting the following error: see below: Did I miss something in the installation? Sorry if I have. Thank you for your help in advance. Liat - FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Kernel info: Darwin 10.8.0 i386 - Please include the following additional information in your report: 1) subject name -2037 2) the entire command-line executed recon-all -i -cw256 MR01 -all -s 2037 3) the error message generated [psmacll1:P1192_freesurfer/2037/7_YNICT1A] liat% recon-all -i -cw256 MR01 -all -s 2037 ERROR: cannot find -cw256 Darwin psmacll1.york.ac.uk 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s exited with ERRORS ___ 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] Senior Lecturer Post at York University
Dear all, A Senior Lecturer Post has now opened at York University, England. https://www22.i-grasp.com/fe/tpl_YorkUni01.asp?newms=jj&id=25711 (https://www22.i-grasp.com/fe/tpl_YorkUni01.asp?newms=jj&id=25711) Senior Lecturer Job referenceUoY00368LocationYork, UKBased atUniversity of York - Heslington CampusGrade8DepartmentPsychologyClosing date25 May 2009 Salary: £44,930 to £52,086 per annum. The Role Applications are invited from established researchers who can enhance current research within the Department. You will have a strong record of published work in the areas of social psychology, behavioural neuroscience, and cognitive neuroscience. Strong applications from researchers in other areas of psychology will also be considered. The Department was ranked in the top 10 in the 2008 Research Assessment Exercise, and has excellent facilities for research including the York Neuroimaging Centre housing MEG, fMRI, and TMS and a well-founded animal laboratory. Informal enquiries can be made to the Head of Department, Professor Susan Gathercole (Tel: 01904 432879, email: sg...@york.ac.uk ). Further information about the department is available athttp://www.york.ac.uk/depts/psych/ (http://www.york.ac.uk/depts/psych/). This post is available from 1 September 2009. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] wiki problem
I am sure you are aware of this problem, but since last week we have been unable to access the FreeSurfer wiki (http://surfer.nmr.mgh.harvard.edu/docs/index.html). Is it down for maintenance? and if so when will it be up again? I have just started using FreeSurfer, hence having major problems without the freesurfer wiki to guide me along. Thank you so much for you help. L ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] wiki problem
Hi Krish, I am afraid we had no joy with either option. No one in lab can get access, we have used both Mozilla Firefox, and Internet Explorer, neither can establish a connection. We never had a problem before. I have tried making changes to my computer firewall, again no joy. Liat - Original Message - From: Krish Subramaniam <[EMAIL PROTECTED]> Date: Tuesday, June 10, 2008 8:01 pm Subject: Re: [Freesurfer] wiki problem > Liat, > > Could you tell us the browser you are using? Because we have been > using the fswiki without problems. ( and I can access fswiki from > my > home, hence we can rule out the case that fswiki is not available > external to our center ) > > https://surfer.nmr.mgh.harvard.edu/fswiki > > and > > http://surfer.nmr.mgh.harvard.edu/fswiki > > both should work with the first one asking you to accept a > certificate. ( secure http connection ) > > -Krish > > On Jun 10, 2008, at 6:52 PM, Liat Levita wrote: > > I am sure you are aware of this problem, but since last week we > have > > been unable to access the FreeSurfer wiki > (http://surfer.nmr.mgh.harvard.edu/docs/index.html > > ). Is it down for maintenance? and if so when will it be up again? > > > > I have just started using FreeSurfer, hence having major > problems > > without the freesurfer wiki to guide me along. > > > > Thank you so much for you help. > > > > L > > > > > > ___ > > 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 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] wiki problem
Dear all, thank you so much for all your help. Problem solved. Cornell was blocking the site for a security reasons, our network guys said they noticed suspicious traffic from that i.p address (the mind boggles ...). They have now unblocked it : ) Liat - Original Message - From: Joe Paxton <[EMAIL PROTECTED]> Date: Wednesday, June 11, 2008 9:34 am Subject: Re: [Freesurfer] wiki problem > Perhaps it is a DNS issue? You could try bypassing DNS by replacing > > the hostname with the ip in the URL: > > http://132.183.202.158/fswiki > or > https://132.183.202.158/fswiki > > If that works, then the problem is likely with DNS at Cornell, in > which case you'll need to contact your network helpdesk. > > On Jun 11, 2008, at 8:31 AM, Liat Levita wrote: > > > Hi Krish, > > > > I am afraid we had no joy with either option. > > > > No one in lab can get access, we have used both Mozilla Firefox, > and > > Internet Explorer, neither can establish a connection. > > > > We never had a problem before. I have tried making changes to my > > computer firewall, again no joy. > > > > Liat > > > > > > - Original Message - > > From: Krish Subramaniam <[EMAIL PROTECTED]> > > Date: Tuesday, June 10, 2008 8:01 pm > > Subject: Re: [Freesurfer] wiki problem > > > >> Liat, > >> > >> Could you tell us the browser you are using? Because we have been > >> using the fswiki without problems. ( and I can access fswiki from > >> my > >> home, hence we can rule out the case that fswiki is not available > >> external to our center ) > >> > >> https://surfer.nmr.mgh.harvard.edu/fswiki > >> > >> and > >> > >> http://surfer.nmr.mgh.harvard.edu/fswiki > >> > >> both should work with the first one asking you to accept a > >> certificate. ( secure http connection ) > >> > >> -Krish > >> > >> On Jun 10, 2008, at 6:52 PM, Liat Levita wrote: > >>> I am sure you are aware of this problem, but since last week we > >> have > >>> been unable to access the FreeSurfer wiki > >> (http://surfer.nmr.mgh.harvard.edu/docs/index.html > >>> ). Is it down for maintenance? and if so when will it be up again? > >>> > >>> I have just started using FreeSurfer, hence having major > >> problems > >>> without the freesurfer wiki to guide me along. > >>> > >>> Thank you so much for you help. > >>> > >>> L > >>> > >>> > >>> ___ > >>> 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 > >> > > > > > > ___ > > 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
[Freesurfer] Prob:Software Download Tiger version \
Hi, I am trying to download the updated FreeSurfer - Mac OS X Tiger (10.4.11) PowerPC stable v4.0.5 15 June 2008 - freesurfer-Darwin-tiger-ppc-stable-pub-v4.0.5-full.dmg However, when I do so I keep getting the zipped Leopard package. I wonder if something is wrong with the link to the tiger version? Liat ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Prob:Software Download Tiger version \
Hi Nick, when it starts downloading you can see it as tiger - but when it finally uploads the package is labeled -freesurfer-Darwin-leopard-full.pkg, which seems very odd. L p.s. I will try wget. Just need to install it on my machine. - Original Message - From: Nick Schmansky <[EMAIL PROTECTED]> Date: Monday, June 16, 2008 12:09 pm Subject: Re: [Freesurfer] Prob:Software Download Tiger version \ > Liat, > > I am unable to recreate what you are seeing. When I click on the > 'freesurfer-Darwin-tiger-ppc-stable-pub-v4.0.5-full.dmg' link > (albeit on > a Linux machine), it downloads that filename. > > You could try: > > wget > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Darwin-tiger- > ppc-stable-pub-v4.0.5-full.dmg > > from a terminal as an alternative. > > Nick > > > On Mon, 2008-06-16 at 11:25 -0400, Liat Levita wrote: > > Hi, I am trying to download the updated FreeSurfer - Mac OS X > Tiger (10.4.11) PowerPC stable v4.0.5 15 June 2008 - freesurfer- > Darwin-tiger-ppc-stable-pub-v4.0.5-full.dmg > > > > However, when I do so I keep getting the zipped Leopard package. > I wonder if something is wrong with the link to the tiger version? > > > > Liat > > > > > > > > > > ___ > > 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 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] X11 - FreeSurfer hot-key problem Mac
Hello, I wonder if anyone else has had this problem on the Mac. I have now installed FreeSurfer (Tiger V4.0.5) on 3 machines, everytime I do this some of my shortcut X11 keys stop working. We are running - X11 1.1.3 - on a Mac OS X 10.4.11 I would really appricate your help with this - Does anyone know how one may fix this. Thank you Liat - Original Message - From: Krish Subramaniam <[EMAIL PROTECTED]> Date: Tuesday, June 17, 2008 12:54 pm Subject: Re: [Freesurfer] tkmedit --> tksurfer (tkmedit points not being saved) > Aaron and Bruce, > > Looks like tkmedit saves edit.dat in the directory from which it is > > invoked, but tksurfer tries to load edit.dat from the tmp/edit.dat > in > the subject dir. > > A simple workaround is to setenv a variable called > FS_SAVE_GOTO_POINT > to a filename where you want both tkmedit and tksurfer to read/save > > the points. Like, > > setenv FS_SAVE_GOTO_POINT /tmp/point.dat > > This should work. > > Anyway, tkmedit should try and save the point to the standard > ( documented ) location /tmp/edit.dat and if it can't > it > should save it to the ./edit.dat... will try and fix this. > > Best, > Krish > > On Jun 16, 2008, at 8:35 PM, Bruce Fischl wrote: > > > the points are stored in the subject's tmp/edit.dat dir. Does > that > > file exist? Is there any error in either of the terminal windows? > > > > On Mon, 16 Jun 2008, Aaron Shmookler wrote: > > > >> Although new to Freesurfer, I have in the past been able to save > > >> points on > >> tkmedit and bring them up on an inflated tksurfer image. > However, > >> now this > >> is not happening. When I click on Save Point or go to > Tools>Save > >> Point in > >> tkmedit, no coordinates are brought up in the tkmedit Terminal > >> window. So, > >> when I try to bring up points on tksurfer (goto saved point) no > >> points are > >> shown. > >> > >> Help would be greatly appreciated. > >> > >> Thanks, > >> Aaron > >> > > ___ > > 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 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: Further questions regarding freesurfer 4.0.5
Hi all, we are also having some problems with v4.05 (Mac computer PC Tiger)
-we keep getting problems with edit segmentation
All seems well until we perform the following sequance of actions:
1. Press mouse button 3 to erase voxels from a particular ROI.
2. Press mouse button 2 to add voxels to a selected ROI (after having chosen
the appropriate label in 'Configure Segmentation Brush' tool option.
3. Then press mouse button 3 to erase voxels (from any region not necessarily
what we have just been working on) - Now instead of just erasing it adds the
label 'nerve' to area that we want to delete.
We have tried playing around with this, and have now gone back to our older
version of freesurfer where this doesn't happen.
We also get the following error message while doing 'Edit Segmentation' which
causes the system to crash.
ErrorLog:
-
syntax error in expression " * 2": unexpected operator *
syntax error in expression " * 2": unexpected operator *
while executing
"expr $nSelection * 2"
(procedure "SendSegBrushInfo" line 11)
invoked from within
"SendSegBrushInfo"
invoked from within
".wwEditSegBrushInfoDlog.lfwFill.border.frame.fwFill.fwSegSrc.rbw invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w $cmd]"
(procedure "tk::CheckRadioInvoke" line 3)
invoked from within
"tk::CheckRadioInvoke
.wwEditSegBrushInfoDlog.lfwFill.border.frame.fwFill.fwSegSrc.rbw"
(command bound to event)
*** *** *** *** ***
Liat Levita, PhD
Instructor of Psychology in Psychiatry
Sackler Institute for Developmental Psychobiology
Weill Medical College of Cornell University
1300 York Ave, Box 140
New York, NY 10021
Tel: 212 746 5836
Fax: 212 746 5755
http://www.sacklerinstitute.org/cornell
- Original Message -
From: Sebastian Moeller <[EMAIL PROTECTED]>
Date: Wednesday, June 18, 2008 4:57 am
Subject: [Freesurfer] questions regarding freesurfer 4.0.5
> First, if this shows up twice, let m apologise for mixing up my
> email
> addresses...
>
> Aloha fellow surfers,
>
>
> I just installed
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Darwin-leopard-
> i686-stable-pub-v4.0.5-full.dmg
> on my:
> intel macbook, running 10.5.3 with 4GB of RAM. A few observations:
> 1) minor: freeview does not seem to be part of the dmg, probably
> expected, but from the release notes it is not obvious, whether the
>
> macos version should contain it or not
> 2) minor, minor: it seems like the whole macos version is built for
>
> 32bit only (at least that is what "file `which mri_convert`" and a
> few
> other binaries tell me); would it be possible to have a 64bit built
>
> (than my macbook might suffice for surface reconstruction as well).
>
> 3) scuba dies horribly (tkmedit and tksurfer, however seem to work,
> at
> least they start up and display something), here is the problem
> report:
> Path:/opt/freesurfer//bin/scuba.bin
> Identifier: scuba.bin
> Version: ??? (???)
> Code Type: X86 (Native)
> Parent Process: tcsh [18243]
>
> Date/Time: 2008-06-18 10:10:42.832 +0200
> OS Version: Mac OS X 10.5.3 (9D34)
> Report Version: 6
>
> Exception Type: EXC_BAD_ACCESS (SIGBUS)
> Exception Codes: KERN_PROTECTION_FAILURE at 0x
> Crashed Thread: 0
>
> Thread 0 Crashed:
> 0 scuba.bin 0x001e5764 0x1000 + 1984356
> 1 dyld 0x8fe0e723
> ImageLoader::recursiveInitialization(ImageLoader::LinkContext
> const&,
> unsigned int) + 307
> 2 dyld 0x8fe0e809
> ImageLoader::runInitializers(ImageLoader::LinkContext const&) + 57
> 3 dyld 0x8fe04102
> dyld::initializeMainExecutable() + 146
> 4 dyld 0x8fe07b5f
> dyld::_main(mach_header
> const*, unsigned long, int, char const**, char const**, char
> const**)
> + 2975
> 5 dyld 0x8fe01872
> dyldbootstrap::start(mach_header const*, int, char const**, long) +
> 8186 dyld 0x8fe01037 _dyld_start + 39
>
> Thread 0 crashed with X86 Thread State (32-bit):
> eax: 0x ebx: 0x001e570c ecx: 0x0002 edx: 0x
> edi: 0x0026 esi: 0x1000 ebp: 0xbfffd548 esp: 0xbfffd4c0
> ss: 0x001f efl: 0x00010282 eip: 0x001e5764 cs: 0x0017
> ds: 0x001f es: 0x001f fs: 0x gs: 0x0037
> cr2: 0x
>
> Binary Images:
>0x1000 - 0x23ffed +scuba.bin ??? (???)
> /opt/freesurfer/bin/scuba.bin
> 0x2af
[Freesurfer] AFNI /freesurfer aseg files problem
Hello,
I wonder if anyone using AFNI converted freesurfer files has come across this
problem (or can tell me if I making an error somewhere that I am just not
seeing right now). I posted the same question on the AFNI board but haven't
gotten feedback as yet.
Here is the problem:
After using freesurfer to get subcortical segmentations, I converted the
resulting freesurfer files to AFNI format, which was fine - I had no problems
doing that. However, when I try use these subcortical segmentation data files
(subjectID_aseg_m_at3+tlrc) as masks to pull put PSC signal from each region of
interest, I am getting an odd effect of right versus left; whereby left
clusters output is fine ( voxel numbers are correct after 3dmaskave), but for
the left it is very wrong. I have checked that the labels of the ROIs I am
using are correct on AFNI GUI and they are. (code and output below)
I am a bit at a loss; any help will be much appreciated.
Liat
AFNI Code used
---
Foreach subj (xxx)
foreach cluster (18 54)
3dmaskave -q -mask ${subj}_aseg_m_at3+tlrc -mrange ${cluster} ${cluster} \
"${subj}_all_runs_pscA_at3+tlrc" > ${subj}_fsROI_PSC_cluster_${cluster}.1D
end
end
Output (get the same odd voxel output from all right hand side of the brain
freesurfer generated ROIs)
---
*For cluster 18 Left Amygdala
++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit]
+++ 37 voxels survive the mask
*For cluster 54 Right Amygdala
++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit]
+++ 200 voxels survive the mask
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Re: [Freesurfer] AFNI /freesurfer aseg files problem
Hi Doug, I just checked, yes they are.
Liat
PS. I attached the Info files to this message.
- Original Message -
From: Doug Greve <[EMAIL PROTECTED]>
Date: Monday, July 28, 2008 12:16 pm
Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem
> are you sure that t1rc and pscA are the same dimension? Remember,
> freesurfer resamples everything into 1mm3, 256^3
>
> doug
>
>
>
> Liat Levita wrote:
>
> >Hello,
> >I wonder if anyone using AFNI converted freesurfer files has come
> across this problem (or can tell me if I making an error somewhere
> that I am just not seeing right now). I posted the same question on
> the AFNI board but haven't gotten feedback as yet.
> >
> >Here is the problem:
> >
> >After using freesurfer to get subcortical segmentations, I
> converted the resulting freesurfer files to AFNI format, which was
> fine - I had no problems doing that. However, when I try use these
> subcortical segmentation data files (subjectID_aseg_m_at3+tlrc) as
> masks to pull put PSC signal from each region of interest, I am
> getting an odd effect of right versus left; whereby left clusters
> output is fine ( voxel numbers are correct after 3dmaskave), but
> for the left it is very wrong. I have checked that the labels of
> the ROIs I am using are correct on AFNI GUI and they are. (code and
> output below)
> >
> >I am a bit at a loss; any help will be much appreciated.
> >
> >Liat
> >
> >AFNI Code used
> >---
> >Foreach subj (xxx)
> >foreach cluster (18 54)
> >3dmaskave -q -mask ${subj}_aseg_m_at3+tlrc -mrange ${cluster}
> ${cluster} \
> >"${subj}_all_runs_pscA_at3+tlrc" >
> ${subj}_fsROI_PSC_cluster_${cluster}.1D
> >end
> >end
> >
> >Output (get the same odd voxel output from all right hand side of
> the brain freesurfer generated ROIs)
> >---
> >*For cluster 18 Left Amygdala
> >++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit]
> >+++ 37 voxels survive the mask
> >
> >*For cluster 54 Right Amygdala
> >++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit]
> >+++ 200 voxels survive the mask
> >
> >
> >
> >
> >___
> >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
> [EMAIL PROTECTED]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
Info_pscA_at3+tlrc
Description: Binary data
info_aseg_m_at+tlrc
Description: Binary data
___
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Re: [Freesurfer] AFNI /freesurfer aseg files problem
Thank you Doug.
I also just got help from the AFNI message board which solved the problem: so
here is a note for AFNI/freesurfer users if they come across this too - if you
run AFNI's @auto_tlrc command use the '-rmode NN' so that it does nearest
neighbor resampling.
- Original Message -
From: Doug Greve <[EMAIL PROTECTED]>
Date: Monday, July 28, 2008 1:37 pm
Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem
> Sorry, don't know anything about those commands. You're probably
> better
> off registering the functional data directly to the anatomical
> (fslregister or spmregister) rather than going thru the talairach
> transform. You can then use mri_vol2vol to map the functional to
> the
> anatomical, then mri_segstats to exctract the average functional
> value
> (or you can probably use the afni command at that point).
>
> doug
>
> Liat Levita wrote:
>
> >Hello Doug,
> >I transformed the aseg_m file to be 3x3x3.
> >I will try and trouble shot the possible error in that transform-
> >
> >The AFNI steps I used to transform the freesurfer files to AFNI
> format, and than to be 3x3x3 are pasted below.
> >
> >Liat
> >
> >-
> >foreach subj (xxx)
> >
> >
> >#step1
> >@SUMA_Make_Spec_FS -sid ${subj}
> >
> >#step2
> >
> >@SUMA_AlignToExperiment \
> >-exp_anat
> /Volumes/cbgb/Liat/freesurfer_subjects/${subj}/SUMA/${subj}_anat+orig \
> >-surf_anat
> /Volumes/cbgb/Liat/freesurfer_subjects/${subj}/SUMA/${subj}_SurfVol+orig \
> >-wd \
> >-prefix ${subj}_AlignExp
> >
> >
> >#step 3: To align a given parcellation file
> >
> >3dWarp -NN -matparent ${subj}_AlignExp+orig -prefix ${subj}_aseg_m
> aseg.nii>
> >#step 4: I transformed the functional data set by the talairch
> transform obtained for the anatomical data, and then which was
> resampled to a 3x3x3 space during this step.
> >
> >@auto_tlrc -apar ${subj}_anat_at+tlrc -input
> ${subj}_FC_Seed_aseg_fs_AMY_stats_ni_pi_Final+orig -dxyz 3 -suffix
> _at3>
> >end
> >
> >
> >
> >
> >
> >- Original Message -
> >From: Doug Greve <[EMAIL PROTECTED]>
> >Date: Monday, July 28, 2008 1:07 pm
> >Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem
> >
> >
> >
> >>I would suspect that something happened when you converted to
> afni
> >>format. The aseg starts out at 1mm3, 256^3, but it appears to be
> >>3mm3,
> >>54x64x50. These conversions are quit tricky and easy to get
> wrong.
> >>Also,
> >>did you check the aseg.stats file to assure that the volumes of
> the
> >>amyg
> >>are more-or-less symetrical?
> >>
> >>doug
> >>
> >>
> >>R-to-L extent: -79.500 [R] -to-79.500 [L] -step- 3.000
> mm
> >>[ 54
> >>voxels]
> >>A-to-P extent: -79.500 [A] -to- 109.500 [P] -step- 3.000
> mm
> >>[ 64
> >>voxels]
> >>I-to-S extent: -63.500 [I] -to-83.500 [S] -step- 3.000
> mm
> >>[ 50
> >>voxels]
> >>
> >>
> >>Liat Levita wrote:
> >>
> >>
> >>
> >>>Hi Doug, I just checked, yes they are.
> >>>
> >>>Liat
> >>>
> >>>PS. I attached the Info files to this message.
> >>>
> >>>
> >>>
> >>>
> >>>- Original Message -
> >>>From: Doug Greve <[EMAIL PROTECTED]>
> >>>Date: Monday, July 28, 2008 12:16 pm
> >>>Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>are you sure that t1rc and pscA are the same dimension?
> Remember,
> >>>>freesurfer resamples everything into 1mm3, 256^3
> >>>>
> >>>>doug
> >>>>
> >>>>
> >>>>
> >>>>Liat Levita wrote:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>Hello,
> >>>>>I wonder if anyone using AFNI converted freesurfer files has
> >>>>>
> >>>>>
> >>come
> >>
> >>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>across this prob
Re: [Freesurfer] AFNI /freesurfer aseg files problem
Hello Doug,
I transformed the aseg_m file to be 3x3x3.
I will try and trouble shot the possible error in that transform-
The AFNI steps I used to transform the freesurfer files to AFNI format, and
than to be 3x3x3 are pasted below.
Liat
-
foreach subj (xxx)
#step1
@SUMA_Make_Spec_FS -sid ${subj}
#step2
@SUMA_AlignToExperiment \
-exp_anat /Volumes/cbgb/Liat/freesurfer_subjects/${subj}/SUMA/${subj}_anat+orig
\
-surf_anat
/Volumes/cbgb/Liat/freesurfer_subjects/${subj}/SUMA/${subj}_SurfVol+orig \
-wd \
-prefix ${subj}_AlignExp
#step 3: To align a given parcellation file
3dWarp -NN -matparent ${subj}_AlignExp+orig -prefix ${subj}_aseg_m aseg.nii
#step 4: I transformed the functional data set by the talairch transform
obtained for the anatomical data, and then which was resampled to a 3x3x3
space during this step.
@auto_tlrc -apar ${subj}_anat_at+tlrc -input
${subj}_FC_Seed_aseg_fs_AMY_stats_ni_pi_Final+orig -dxyz 3 -suffix _at3
end
- Original Message -
From: Doug Greve <[EMAIL PROTECTED]>
Date: Monday, July 28, 2008 1:07 pm
Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem
>
> I would suspect that something happened when you converted to afni
> format. The aseg starts out at 1mm3, 256^3, but it appears to be
> 3mm3,
> 54x64x50. These conversions are quit tricky and easy to get wrong.
> Also,
> did you check the aseg.stats file to assure that the volumes of the
> amyg
> are more-or-less symetrical?
>
> doug
>
>
> R-to-L extent: -79.500 [R] -to-79.500 [L] -step- 3.000 mm
> [ 54
> voxels]
> A-to-P extent: -79.500 [A] -to- 109.500 [P] -step- 3.000 mm
> [ 64
> voxels]
> I-to-S extent: -63.500 [I] -to- 83.500 [S] -step- 3.000 mm
> [ 50
> voxels]
>
>
> Liat Levita wrote:
>
> >Hi Doug, I just checked, yes they are.
> >
> >Liat
> >
> >PS. I attached the Info files to this message.
> >
> >
> >
> >
> >- Original Message -
> >From: Doug Greve <[EMAIL PROTECTED]>
> >Date: Monday, July 28, 2008 12:16 pm
> >Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem
> >
> >
> >
> >>are you sure that t1rc and pscA are the same dimension? Remember,
> >>freesurfer resamples everything into 1mm3, 256^3
> >>
> >>doug
> >>
> >>
> >>
> >>Liat Levita wrote:
> >>
> >>
> >>
> >>>Hello,
> >>>I wonder if anyone using AFNI converted freesurfer files has
> come
> >>>
> >>>
> >>across this problem (or can tell me if I making an error
> somewhere
> >>that I am just not seeing right now). I posted the same question
> on
> >>the AFNI board but haven't gotten feedback as yet.
> >>
> >>
> >>>Here is the problem:
> >>>
> >>>After using freesurfer to get subcortical segmentations, I
> >>>
> >>>
> >>converted the resulting freesurfer files to AFNI format, which
> was
> >>fine - I had no problems doing that. However, when I try use
> these
> >>subcortical segmentation data files (subjectID_aseg_m_at3+tlrc)
> as
> >>masks to pull put PSC signal from each region of interest, I am
> >>getting an odd effect of right versus left; whereby left clusters
> >>output is fine ( voxel numbers are correct after 3dmaskave), but
> >>for the left it is very wrong. I have checked that the labels of
> >>the ROIs I am using are correct on AFNI GUI and they are. (code
> and
> >>output below)
> >>
> >>
> >>>I am a bit at a loss; any help will be much appreciated.
> >>>
> >>>Liat
> >>>
> >>>AFNI Code used
> >>>---
> >>>Foreach subj (xxx)
> >>>foreach cluster (18 54)
> >>>3dmaskave -q -mask ${subj}_aseg_m_at3+tlrc -mrange ${cluster}
> >>>
> >>>
> >>${cluster} \
> >>
> >>
> >>>"${subj}_all_runs_pscA_at3+tlrc" >
> >>>
> >>>
> >>${subj}_fsROI_PSC_cluster_${cluster}.1D
> >>
> >>
> >>>end
> >>>end
> >>>
> >>>Output (get the same odd voxel output from all right hand side
> of
> >>>
> >>>
> >>the brain freesurfer generated ROIs)
> >>
> >>
> >>>---
> >>>*For cluster 18 Left Amygdala
> >>>++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul
