RE: [Freesurfer] want to view one segmented subcortical object at a time...
depends what you mean. You can do group analysis of structure volumes, but visualizing that is a matter of bar charts and such. We also have some tools for making "density" measures, but those aren't integrated into the distributed version yet. cheers, Bruce On Tue, 21 Mar 2006, Goradia, Dhruman D wrote: Hello Bruce and all, Is it possible to perform group analysis based only on a particular subcortical region of interest and visualize it? -Dhruman -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl Sent: Monday 20 March 2006 16:20 To: Shahabuddin Ansari Cc: freesurfer@nmr.mgh.harvard.edu; Steve Pieper Subject: Re: [Freesurfer] want to view one segmented subcortical object ata time... Hi Shahab, we don't have anything to do that, although I think slicer probably can do it with our data. Bruce On Mon, 20 Mar 2006, Shahabuddin Ansari wrote: Hello, I have segmented subcortical regions of the whole brain from Freesurfer. Can somebody help me how to view one object (say right hippocampus) at a time. Thanks Shahab __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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
RE: [Freesurfer] want to view one segmented subcortical object at a time...
Hello Bruce and all, Is it possible to perform group analysis based only on a particular subcortical region of interest and visualize it? -Dhruman -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl Sent: Monday 20 March 2006 16:20 To: Shahabuddin Ansari Cc: freesurfer@nmr.mgh.harvard.edu; Steve Pieper Subject: Re: [Freesurfer] want to view one segmented subcortical object ata time... Hi Shahab, we don't have anything to do that, although I think slicer probably can do it with our data. Bruce On Mon, 20 Mar 2006, Shahabuddin Ansari wrote: > Hello, > > I have segmented subcortical regions of the whole > brain from Freesurfer. Can somebody help me how to > view one object (say right hippocampus) at a time. > > Thanks > Shahab > > __ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > ___ > 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] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data
Hi Aaron, don't bother looking at the orig - look at the white and pial instead. The pial in your image looks fine. Bruce On Tue, 21 Mar 2006, Goldman, Aaron (NIH/NIMH) [C] wrote: Hi, I'm using stable 3.0 with the recon-all -all command (so whichever atlas is the default for lh.aparc.annot). I'm not sure if this is what your 2nd question is asking, but the pial outlines do tend to "cross under" the orig slightly (as shown above). I kind of assumed this was normal though. Anyway, I've looked at some more, and when I look at the orig surface I think most of ours look like the image Greg posted. Were you able to answer his question (if so, I don't think it went to the list)? Thanks, Aaron -Original Message- From: Rahul Desikan [mailto:[EMAIL PROTECTED] Sent: Monday, March 20, 2006 2:20 PM To: Goldman, Aaron (NIH/NIMH) [C] Cc: Greg Harris; Freesurfer Mailing List; Karl Helmer Subject: RE: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data Hi Aaron, Which version of Freesurfer and which version of the parc atlas are you using? Also have you checked your surfaces along the midline to see if they are acting in a strange way (i.e. self-intersecting, crossing the midline, etc.)? thanks, Rahul On Mon, 20 Mar 2006, Goldman, Aaron (NIH/NIMH) [C] wrote: Hi, I think I may have observed the same issue he's talking about. What I've attached is possibly an extreme example (I haven't inspected many yet, to be honest), but it seems typical for at least a bit of this to happen in our subjects. I was also curious if the black "unknown" label was expected to extend into the temporal lobe as it does here. Thanks, -Aaron- -Original Message- From: Rahul Desikan [mailto:[EMAIL PROTECTED] Sent: Saturday, March 18, 2006 5:51 PM To: Greg Harris Cc: Freesurfer Mailing List; Karl Helmer Subject: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data Hi Greg, Could you send along jpegs or rgbs detailing what excactly the parcellation atlas is doing in the cingulate region? Also have you looked at both the white and pial surfaces in this area? Hope you are well othwerwise, Rahul On Sat, 18 Mar 2006, Greg Harris wrote: Dear Karl, Has anybody had any success with the midline rois given by the atlas curvature.buckner40.filled.desikan_killiany that is automatically applied by autorecon3 under the newest stable release, version 3.0? Our trouble lies in the regions labeled corpuscallosum and cingulate: this atlas is giving us a corpus callosum that is exactly the ventral cingulate sulcus, and the 4 cingulate gyrus segments, which is what we are interested in in this case, incorrectly exclude their ventral portion. I presume this has been made to work at mgh, because Rahul Desikan's paper contains an illustration that is anatomically correctly labeled for these regions. We are providing an orig/001.mgz image to the autorecon1 step that is talairach aligned, skull stripped, and resampled to 1.0 mm voxels, but otherwise is a signed 16-bit T1-weighted MRI scan. We have thousands of them, collected over the past 15 years. We are writing a nifti .nii file, and converting it with mri_convert -it nii -ic 128 128 96 -oc 128 128 96 -iid -1.0 0.0 0.0 /raid1/structural/MR/9517294/0036195/10_ACPC/0036195_10_T1_brain.nii /raid1/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects/IowaFifty_2005_0036195/mri/orig/001.mgz We actually mean to numerically measure the extent -- the area and thickness, say -- of anatomical regions of interest including cingulate and apply statistical tests to these data. A line of guff about Type I and Type II errors and what is only presumable when identifying anatomical rois would be of no interest, and considered needlessly defensive. After all, the other 29 regions of Desikan's really great atlas are in working order! Do we need to convince Rahul Desikan to release the "correct" *h.curvature.buckner40.filled.desikan_killiany.gcs files with FreeSurfer 3.0 that correspond to his paper? Greg Harris The University of Iowa College of Medicine Psychiatry NeuroImaging Lab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data
Hi, I'm using stable 3.0 with the recon-all -all command (so whichever atlas is the default for lh.aparc.annot). I'm not sure if this is what your 2nd question is asking, but the pial outlines do tend to "cross under" the orig slightly (as shown above). I kind of assumed this was normal though. Anyway, I've looked at some more, and when I look at the orig surface I think most of ours look like the image Greg posted. Were you able to answer his question (if so, I don't think it went to the list)? Thanks, Aaron -Original Message- From: Rahul Desikan [mailto:[EMAIL PROTECTED] Sent: Monday, March 20, 2006 2:20 PM To: Goldman, Aaron (NIH/NIMH) [C] Cc: Greg Harris; Freesurfer Mailing List; Karl Helmer Subject: RE: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data Hi Aaron, Which version of Freesurfer and which version of the parc atlas are you using? Also have you checked your surfaces along the midline to see if they are acting in a strange way (i.e. self-intersecting, crossing the midline, etc.)? thanks, Rahul On Mon, 20 Mar 2006, Goldman, Aaron (NIH/NIMH) [C] wrote: > Hi, I think I may have observed the same issue he's talking about. What I've > attached is possibly an extreme example (I haven't inspected many yet, to be > honest), but it seems typical for at least a bit of this to happen in our > subjects. I was also curious if the black "unknown" label was expected to > extend into the temporal lobe as it does here. > > Thanks, > > -Aaron- > > -Original Message- > From: Rahul Desikan [mailto:[EMAIL PROTECTED] > Sent: Saturday, March 18, 2006 5:51 PM > To: Greg Harris > Cc: Freesurfer Mailing List; Karl Helmer > Subject: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' > with skull-stripped orig data > > Hi Greg, > > Could you send along jpegs or rgbs detailing what excactly the > parcellation atlas is doing in the cingulate region? Also have you looked > at both the white and pial surfaces in this area? > > Hope you are well othwerwise, > > Rahul > > On Sat, 18 Mar 2006, Greg Harris wrote: > >> Dear Karl, >> >> Has anybody had any success with the midline rois given by the atlas >> curvature.buckner40.filled.desikan_killiany that is automatically applied >> by autorecon3 under the newest stable release, version 3.0? >> >> Our trouble lies in the regions labeled corpuscallosum and >> cingulate: this >> atlas is giving us a corpus callosum that is exactly the ventral cingulate >> sulcus, and the 4 >> cingulate gyrus segments, which is what we are interested in in this case, >> incorrectly >> exclude their ventral portion. >> >> I presume this has been made to work at mgh, because Rahul Desikan's paper >> contains >> an illustration that is anatomically correctly labeled for these regions. >> >> We are providing an orig/001.mgz image to the autorecon1 step that is >> talairach aligned, >> skull stripped, and resampled to 1.0 mm voxels, but otherwise is a signed >> 16-bit >> T1-weighted MRI scan. We have thousands of them, collected over the past 15 >> years. >> We are writing a nifti .nii file, and converting it with >> >> mri_convert -it nii -ic 128 128 96 -oc 128 128 96 -iid -1.0 0.0 0.0 >> /raid1/structural/MR/9517294/0036195/10_ACPC/0036195_10_T1_brain.nii >> /raid1/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects/IowaFifty_2005_0036195/mri/orig/001.mgz >> >> We actually mean to numerically measure the extent -- the area and thickness, >> say -- of >> anatomical regions of interest including cingulate and apply >> statistical tests to >> these data. A line of guff about Type I and Type II errors and what is only >> presumable >> when identifying anatomical rois would be of no interest, and considered >> needlessly >> defensive. After all, the other 29 regions of Desikan's really great atlas >> are in working >> order! >> >> Do we need to convince Rahul Desikan to release the "correct" >> *h.curvature.buckner40.filled.desikan_killiany.gcs files with FreeSurfer 3.0 >> that correspond to his paper? >> >> Greg Harris >> The University of Iowa College of Medicine >> Psychiatry NeuroImaging Lab >> >> >> > > -- <> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FSL/Freesurfer
Title: FSL/Freesurfer
I believe that I have read a post on this in the past, but I was unable to run a search. I have FSL configured to startup in X11 without a problem. Also can run Freesurfer (source SetupFreeSurfer.csh) without a problem. But FSL will not work after I have ran the source SetUpFreeSurfer.csh command. The following is the error output. Any work around besides run separate X11 windows for FSL and Freesurfer?
[Clifford-Smiths-Computer:~] Cliff% source SetUpFreeSurfer.csh
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Users/Cliff/Imaging/freesurfer
FSFAST_HOME /Users/Cliff/Imaging/freesurfer/fsfast
SUBJECTS_DIR /Users/Cliff/Imaging/freesurfer/subjects
FUNCTIONALS_DIR /Users/Cliff/Imaging/freesurfer/sessions
MINC_BIN_DIR /Users/Cliff/Imaging/freesurfer/mni/bin
MINC_LIB_DIR /Users/Cliff/Imaging/freesurfer/mni/lib
PERL5LIB /Users/Cliff/Imaging/freesurfer/mni/lib/../System/Library/Perl/5
.8.6
GSL_DIR /Users/Cliff/Imaging/freesurfer/lib/gsl
QTDIR /Users/Cliff/Imaging/freesurfer/lib/qt
TCLLIBPATH /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib
MISC_LIB /Users/Cliff/Imaging/freesurfer/lib/misc/lib
FSL_DIR /users/cliff/fsl
[Clifford-Smiths-Computer:~] Cliff% fsl
Error in startup script: no suitable image found. Did find:
/Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0
x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A
/Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0
x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A
while executing
"load /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix"
("package ifneeded" script)
invoked from within
"package require Tix"
invoked from within
"if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] != 0 } {
package require Tix
tix configure -scheme TixGray
option add ..."
(file "/users/cliff/fsl/tcl/fslstart.tcl" line 3)
invoked from within
"source [ file dirname [ info script ] ]/fslstart.tcl"
(file "/users/cliff/fsl/tcl/fsl.tcl" line 71)
invoked from within
"source ${FSLDIR}/tcl/${origname}.tcl"
(file "/users/cliff/fsl/bin/fsl" line 19)
[Clifford-Smiths-Computer:~] Cliff%
--
Clifford Smith, PhD
Assistant Professor of Behavioral Sciences
Rush University Medical Center
312.942.2893
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSL/Freesurfer
Hi - I suspect that the simplest solution is to source the FreeSurfer
setup _before_ the FSl setup.
Cheers, Steve.
On 21 Mar 2006, at 16:36, Clifford A. Smith, PhD wrote:
I believe that I have read a post on this in the past, but I was
unable to run a search. I have FSL configured to startup in X11
without a problem. Also can run Freesurfer (source
SetupFreeSurfer.csh) without a problem. But FSL will not work
after I have ran the source SetUpFreeSurfer.csh command. The
following is the error output. Any work around besides run
separate X11 windows for FSL and Freesurfer?
[Clifford-Smiths-Computer:~] Cliff% source SetUpFreeSurfer.csh
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Users/Cliff/Imaging/freesurfer
FSFAST_HOME /Users/Cliff/Imaging/freesurfer/fsfast
SUBJECTS_DIR/Users/Cliff/Imaging/freesurfer/subjects
FUNCTIONALS_DIR /Users/Cliff/Imaging/freesurfer/sessions
MINC_BIN_DIR/Users/Cliff/Imaging/freesurfer/mni/bin
MINC_LIB_DIR/Users/Cliff/Imaging/freesurfer/mni/lib
PERL5LIB/Users/Cliff/Imaging/freesurfer/mni/lib/../System/
Library/Perl/5
.8.6
GSL_DIR /Users/Cliff/Imaging/freesurfer/lib/gsl
QTDIR /Users/Cliff/Imaging/freesurfer/lib/qt
TCLLIBPATH /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib
MISC_LIB/Users/Cliff/Imaging/freesurfer/lib/misc/lib
FSL_DIR /users/cliff/fsl
[Clifford-Smiths-Computer:~] Cliff% fsl
Error in startup script: no suitable image found. Did find:
/Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/
libtix8.1.8.4.a: unknown file type, first eight bytes: 0
x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A
/Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/
libtix8.1.8.4.a: unknown file type, first eight bytes: 0
x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A
while executing
"load /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/
libtix8.1.8.4.a Tix"
("package ifneeded" script)
invoked from within
"package require Tix"
invoked from within
"if { [ string first tclsh [ file tail [ info
nameofexecutable ] ] ] != 0 } {
package require Tix
tix configure -scheme TixGray
option add ..."
(file "/users/cliff/fsl/tcl/fslstart.tcl" line 3)
invoked from within
"source [ file dirname [ info script ] ]/fslstart.tcl"
(file "/users/cliff/fsl/tcl/fsl.tcl" line 71)
invoked from within
"source ${FSLDIR}/tcl/${origname}.tcl"
(file "/users/cliff/fsl/bin/fsl" line 19)
[Clifford-Smiths-Computer:~] Cliff%
--
Clifford Smith, PhD
Assistant Professor of Behavioral Sciences
Rush University Medical Center
312.942.2893
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[EMAIL PROTECTED]http://www.fmrib.ox.ac.uk/~steve
---
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSL/Freesurfer
Clifford,
After sourcing SetUpFreeSurfer.csh, but before starting FSL, type this:
unsetenv TCLLIBPATH
This should take care of the problem you are seeing. You may want to
include that line in your SetUpFreeSurfer.csh file.
Nick
On Tue, 2006-03-21 at 10:36 -0600, Clifford A. Smith, PhD wrote:
> I believe that I have read a post on this in the past, but I was
> unable to run a search. I have FSL configured to startup in X11
> without a problem. Also can run Freesurfer (source
> SetupFreeSurfer.csh) without a problem. But FSL will not work after I
> have ran the source SetUpFreeSurfer.csh command. The following is the
> error output. Any work around besides run separate X11 windows for
> FSL and Freesurfer?
>
>
> [Clifford-Smiths-Computer:~] Cliff% source SetUpFreeSurfer.csh
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME /Users/Cliff/Imaging/freesurfer
> FSFAST_HOME /Users/Cliff/Imaging/freesurfer/fsfast
> SUBJECTS_DIR/Users/Cliff/Imaging/freesurfer/subjects
> FUNCTIONALS_DIR /Users/Cliff/Imaging/freesurfer/sessions
> MINC_BIN_DIR/Users/Cliff/Imaging/freesurfer/mni/bin
> MINC_LIB_DIR/Users/Cliff/Imaging/freesurfer/mni/lib
> PERL5LIB
>/Users/Cliff/Imaging/freesurfer/mni/lib/../System/Library/Perl/5
> .8.6
> GSL_DIR /Users/Cliff/Imaging/freesurfer/lib/gsl
> QTDIR /Users/Cliff/Imaging/freesurfer/lib/qt
> TCLLIBPATH /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib
> MISC_LIB/Users/Cliff/Imaging/freesurfer/lib/misc/lib
> FSL_DIR /users/cliff/fsl
> [Clifford-Smiths-Computer:~] Cliff% fsl
> Error in startup script: no suitable image found. Did find:
> /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a:
> unknown file type, first eight bytes: 0
> x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A
> /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a:
> unknown file type, first eight bytes: 0
> x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A
> while executing
> "load /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix"
> ("package ifneeded" script)
> invoked from within
> "package require Tix"
> invoked from within
> "if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] !
> = 0 } {
> package require Tix
> tix configure -scheme TixGray
> option add ..."
> (file "/users/cliff/fsl/tcl/fslstart.tcl" line 3)
> invoked from within
> "source [ file dirname [ info script ] ]/fslstart.tcl"
> (file "/users/cliff/fsl/tcl/fsl.tcl" line 71)
> invoked from within
> "source ${FSLDIR}/tcl/${origname}.tcl"
> (file "/users/cliff/fsl/bin/fsl" line 19)
> [Clifford-Smiths-Computer:~] Cliff%
>
> --
> Clifford Smith, PhD
> Assistant Professor of Behavioral Sciences
> Rush University Medical Center
> 312.942.2893
>
> ___
> 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] FSL/Freesurfer
That was it. Thanks so much. Just added the unsetenv line to my .cshrc
file.
Cliff
--
Clifford Smith, PhD
Assistant Professor of Behavioral Sciences
Rush University Medical Center
312.942.2893
> From: Nick Schmansky <[EMAIL PROTECTED]>
> Date: Tue, 21 Mar 2006 12:28:43 -0500
> To: "Clifford A. Smith, PhD" <[EMAIL PROTECTED]>
> Cc: Freesurfer Mailing List
> Subject: Re: [Freesurfer] FSL/Freesurfer
>
> Clifford,
>
> After sourcing SetUpFreeSurfer.csh, but before starting FSL, type this:
>
> unsetenv TCLLIBPATH
>
> This should take care of the problem you are seeing. You may want to
> include that line in your SetUpFreeSurfer.csh file.
>
> Nick
>
> On Tue, 2006-03-21 at 10:36 -0600, Clifford A. Smith, PhD wrote:
>> I believe that I have read a post on this in the past, but I was
>> unable to run a search. I have FSL configured to startup in X11
>> without a problem. Also can run Freesurfer (source
>> SetupFreeSurfer.csh) without a problem. But FSL will not work after I
>> have ran the source SetUpFreeSurfer.csh command. The following is the
>> error output. Any work around besides run separate X11 windows for
>> FSL and Freesurfer?
>>
>>
>> [Clifford-Smiths-Computer:~] Cliff% source SetUpFreeSurfer.csh
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME /Users/Cliff/Imaging/freesurfer
>> FSFAST_HOME /Users/Cliff/Imaging/freesurfer/fsfast
>> SUBJECTS_DIR/Users/Cliff/Imaging/freesurfer/subjects
>> FUNCTIONALS_DIR /Users/Cliff/Imaging/freesurfer/sessions
>> MINC_BIN_DIR/Users/Cliff/Imaging/freesurfer/mni/bin
>> MINC_LIB_DIR/Users/Cliff/Imaging/freesurfer/mni/lib
>> PERL5LIB
>>/Users/Cliff/Imaging/freesurfer/mni/lib/../System/Library/Perl/5
>> .8.6
>> GSL_DIR /Users/Cliff/Imaging/freesurfer/lib/gsl
>> QTDIR /Users/Cliff/Imaging/freesurfer/lib/qt
>> TCLLIBPATH /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib
>> MISC_LIB/Users/Cliff/Imaging/freesurfer/lib/misc/lib
>> FSL_DIR /users/cliff/fsl
>> [Clifford-Smiths-Computer:~] Cliff% fsl
>> Error in startup script: no suitable image found. Did find:
>> /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a:
>> unknown file type, first eight bytes: 0
>> x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A
>> /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a:
>> unknown file type, first eight bytes: 0
>> x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A
>> while executing
>> "load /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a
>> Tix"
>> ("package ifneeded" script)
>> invoked from within
>> "package require Tix"
>> invoked from within
>> "if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] !
>> = 0 } {
>> package require Tix
>> tix configure -scheme TixGray
>> option add ..."
>> (file "/users/cliff/fsl/tcl/fslstart.tcl" line 3)
>> invoked from within
>> "source [ file dirname [ info script ] ]/fslstart.tcl"
>> (file "/users/cliff/fsl/tcl/fsl.tcl" line 71)
>> invoked from within
>> "source ${FSLDIR}/tcl/${origname}.tcl"
>> (file "/users/cliff/fsl/bin/fsl" line 19)
>> [Clifford-Smiths-Computer:~] Cliff%
>>
>> --
>> Clifford Smith, PhD
>> Assistant Professor of Behavioral Sciences
>> Rush University Medical Center
>> 312.942.2893
>>
>> ___
>> 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] autorecon2 failures
Hey All, I have a few scans that I've been attempting to process that fail during autorecon2. I've eliminated all scan acquisitions that looked potentially problematic and attempted to rerun them. They both seem to go through autorecon1 without incident. The errors I'm getting are the somewhat ambiguous segmentation fault so I'm really not sure what manaul interventions should be attempted or might be useful to get them to run. Any suggestions would be greatly appreciated. Scans: /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991101rl-new/ /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991122so-new/ Thanks Eliz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] autorecon2 failures
Yes that's exactly what's happening. Well I'm sorry to hear that this is endemic now :(, but I'm glad I'm not crazy ... On Tue, 21 Mar 2006, Bruce Fischl wrote: Hi Eliz, are they faulting in the middle of mri_ca_register? We've just started to have this problem (despite successfully running it on our 80 hemisphere test set!), and I'm tracking it down. sorry :< Bruce On Tue, 21 Mar 2006, Elizabeth Fenstermacher wrote: Hey All, I have a few scans that I've been attempting to process that fail during autorecon2. I've eliminated all scan acquisitions that looked potentially problematic and attempted to rerun them. They both seem to go through autorecon1 without incident. The errors I'm getting are the somewhat ambiguous segmentation fault so I'm really not sure what manaul interventions should be attempted or might be useful to get them to run. Any suggestions would be greatly appreciated. Scans: /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991101rl-new/ /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991122so-new/ Thanks Eliz ___ 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] autorecon2 failures
Hi Eliz, are they faulting in the middle of mri_ca_register? We've just started to have this problem (despite successfully running it on our 80 hemisphere test set!), and I'm tracking it down. sorry :< Bruce On Tue, 21 Mar 2006, Elizabeth Fenstermacher wrote: Hey All, I have a few scans that I've been attempting to process that fail during autorecon2. I've eliminated all scan acquisitions that looked potentially problematic and attempted to rerun them. They both seem to go through autorecon1 without incident. The errors I'm getting are the somewhat ambiguous segmentation fault so I'm really not sure what manaul interventions should be attempted or might be useful to get them to run. Any suggestions would be greatly appreciated. Scans: /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991101rl-new/ /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991122so-new/ Thanks Eliz ___ 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] autorecon2 failures
There is a known bug in the dev environment (at the NMR center). It is recommended to use the stable environment: source /usr/local/freesurfer/nmr-std-env On Tue, 2006-03-21 at 14:16 -0500, Elizabeth Fenstermacher wrote: > Hey All, > > I have a few scans that I've been attempting to process that fail during > autorecon2. I've eliminated all scan acquisitions that looked potentially > problematic and attempted to rerun them. They both seem to go through > autorecon1 without incident. The errors I'm getting are the somewhat > ambiguous > segmentation fault so I'm really not sure what manaul interventions should be > attempted or might be useful to get them to run. Any suggestions would be > greatly appreciated. > > Scans: > /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991101rl-new/ > /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991122so-new/ > > Thanks > Eliz > ___ > 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] autorecon2 failures
what version are you using? On Tue, 21 Mar 2006, Elizabeth Fenstermacher wrote: Yes that's exactly what's happening. Well I'm sorry to hear that this is endemic now :(, but I'm glad I'm not crazy ... On Tue, 21 Mar 2006, Bruce Fischl wrote: Hi Eliz, are they faulting in the middle of mri_ca_register? We've just started to have this problem (despite successfully running it on our 80 hemisphere test set!), and I'm tracking it down. sorry :< Bruce On Tue, 21 Mar 2006, Elizabeth Fenstermacher wrote: Hey All, I have a few scans that I've been attempting to process that fail during autorecon2. I've eliminated all scan acquisitions that looked potentially problematic and attempted to rerun them. They both seem to go through autorecon1 without incident. The errors I'm getting are the somewhat ambiguous segmentation fault so I'm really not sure what manaul interventions should be attempted or might be useful to get them to run. Any suggestions would be greatly appreciated. Scans: /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991101rl-new/ /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991122so-new/ Thanks Eliz ___ 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] total intracranial volume question
Hello, I'm writing because I am trying out some structure-function analyses and I would like to normalize my label volume measurements with the total intracranial volume. I was informed that this value is in /stats/aseg.stats. I was surprised at the range of TIVs that I saw in my 29 subjects (from 1400cm^3 to 2500cm^3). so I looked up what the normative values are for TIV, and it appears that the TIVs estimated for my group are irregular given the standard mean TIV and normal variance. (from one paper that I looked at it seems like the avereage TIV is around 1500cm^3 and that typical variation is measured in the 10-100cm^3 range, not an order of magnitude more than that.) Does anyone have any experience with the estimated TIV and what to expect as a normal range / how to know when something is wrong? Thanks so much! Best, Eli Diamond ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] autorecon2 failures
Hey Bruce, I had been using the dev environment, but I'm rerunning them now in the stable per Nick's suggestion. I didn't realize that it was an established, if relatively new, bug because I hadn't had problems before. Eliz On Tue, 21 Mar 2006, Bruce Fischl wrote: what version are you using? On Tue, 21 Mar 2006, Elizabeth Fenstermacher wrote: Yes that's exactly what's happening. Well I'm sorry to hear that this is endemic now :(, but I'm glad I'm not crazy ... On Tue, 21 Mar 2006, Bruce Fischl wrote: Hi Eliz, are they faulting in the middle of mri_ca_register? We've just started to have this problem (despite successfully running it on our 80 hemisphere test set!), and I'm tracking it down. sorry :< Bruce On Tue, 21 Mar 2006, Elizabeth Fenstermacher wrote: Hey All, I have a few scans that I've been attempting to process that fail during autorecon2. I've eliminated all scan acquisitions that looked potentially problematic and attempted to rerun them. They both seem to go through autorecon1 without incident. The errors I'm getting are the somewhat ambiguous segmentation fault so I'm really not sure what manaul interventions should be attempted or might be useful to get them to run. Any suggestions would be greatly appreciated. Scans: /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991101rl-new/ /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991122so-new/ Thanks Eliz ___ 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] autorecon2 failures
Hi Eliz, you're better of using stable for exactly this reason - we've tested it extensively and it works quite well. Dev is on the other hand definitely *not* stable. Bruce On Tue, 21 Mar 2006, Elizabeth Fenstermacher wrote: Hey Bruce, I had been using the dev environment, but I'm rerunning them now in the stable per Nick's suggestion. I didn't realize that it was an established, if relatively new, bug because I hadn't had problems before. Eliz On Tue, 21 Mar 2006, Bruce Fischl wrote: what version are you using? On Tue, 21 Mar 2006, Elizabeth Fenstermacher wrote: Yes that's exactly what's happening. Well I'm sorry to hear that this is endemic now :(, but I'm glad I'm not crazy ... On Tue, 21 Mar 2006, Bruce Fischl wrote: Hi Eliz, are they faulting in the middle of mri_ca_register? We've just started to have this problem (despite successfully running it on our 80 hemisphere test set!), and I'm tracking it down. sorry :< Bruce On Tue, 21 Mar 2006, Elizabeth Fenstermacher wrote: Hey All, I have a few scans that I've been attempting to process that fail during autorecon2. I've eliminated all scan acquisitions that looked potentially problematic and attempted to rerun them. They both seem to go through autorecon1 without incident. The errors I'm getting are the somewhat ambiguous segmentation fault so I'm really not sure what manaul interventions should be attempted or might be useful to get them to run. Any suggestions would be greatly appreciated. Scans: /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991101rl-new/ /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991122so-new/ Thanks Eliz ___ 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] Problem with overlay of EPI analyze volume over T1 analyze volume in free surfer
Hi, I have been working with an image dataset of EPI images and MR images that have been registered in the freesurfer (transformation for which is stored in a .reg file). A T1 mgz volume was made using the following command: mri_convert -it analyze -ot mgh -i T1001.img -o T1.mgz I formed the EPI volume using the following command: mri_convert -it analyze -ot mgh -i F0001.img -o BH1.mgz when I load the T1 volume, and then overlay the EPI volume in tkmedit, with the reg file for transformation, I get a yellow box superimposed over a T1 image. The EPI volume itself appears to be properly formed, as I can read it directly into freesurfer and get a properly formed image. Was wondering if anyone had any suggestions as to what may be going wrong? Thanks, Salil Soman [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Faster and Parallel recon-all
Hi Daniel, I was having a second look at the script and apparently the script is fine with a small spelling error. The STAT variable which is set at 3 different instances has spelling error in "scripts" where "t" is missing. Once this was corrected the script is fine but it's still not working. It initiates all the processes and then just sits idle. After waiting for half an hour it still does not make step1-00.done (I start directly with motion cor) keeping all the other processes waiting. I am still probing into this. If you can think of something that might be of help then let me know. -Dhruman -Original Message- From: Daniel Goldenholz [mailto:[EMAIL PROTECTED] Sent: Tuesday 21 March 2006 11:25 To: Goradia, Dhruman D Subject: Re: [Freesurfer] Faster and Parallel recon-all Dhruman That's confusing. I think you should take one line of executable code from your script that produces that behavior and then email it to the freesurfer list. It sounds to me like the recon-all script ASSUMES that the log file exists if you specify a name. I thought it actually creates one first, but I could have been mistaken there, and if so I will need to add a few extra lines of code. PLEASE follow up on this. It will help others. The other thing to try is to create a text file first, such as like this: echo "#Starting recon-all manually..." > /Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.log and then see if my script is ok. Keep me posted. D Goradia, Dhruman D wrote: >Hi Daniel, >I tried to use the script super-recon on mac OX S using bash shell. I >made the necessary changes to make it operable in bash. However when I >run the script its gives me the following error: > >Tcsh:/Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.lo g >:not a file or directory. > >I tried to run the first 3 steps of the script (motioncor, >nuintensitycor, talairach) and it gives the above error. However if I >remove the log and status flags, the first 3 steps executes properly. Do >you have any idea why? Do you see any problem if I delete the log and >status flags from the whole script and use it? >-Dhruman > >-Original Message- >From: [EMAIL PROTECTED] >[mailto:[EMAIL PROTECTED] On Behalf Of Daniel >Goldenholz >Sent: Thursday 16 March 2006 15:17 >Cc: Freesurfer Mailing List; Nick Schmansky >Subject: Re: [Freesurfer] Faster and Parallel recon-all > >Ah. Silly me, I didn't notice the -log and -status options. Thanks Nick. > >I have now included those into my super-recon script as well. Problem >solved. > >(if you have seen my script already, you may need to hit RELOAD on your >browser to see the new version) >Daniel > > > >>Nick Schmansky wrote: >> >> >> >>>The script looks good. The one thing it needs though is for the >>> >>> >right > > >>>and left hemi steps to log to separate files, otherwise output to >>> >>> >recon- > > >>>all.log will be interleaved, making debugging impossible. >>> >>>On Thu, 2006-03-16 at 12:15 -0500, Daniel Goldenholz wrote: >>> >>> >>> >>> Ooops. I sent the below with the wrong subject tag. Here it is >again: > > Daniel Goldenholz wrote: >Freesurfers > >I was hoping someone else would do this, but well, it seems that no > > > > > >one did. So I went ahead and made this myself. >Amusingly, I don't NEED to reconstruct any brains right now, so I >don't have anything to test this out with. >Please someone try it, and let me know if it is helpful. > >What I did was write a script that runs each and every part of the >recon-all -all stream, one command at a time. (based on the NEW >version 3 stream). >Each one is loaded with -waitfor and -notify so that the dependency > > > > > >structure is intact. >However, ALL of the commands start running in the background! If >you have a 2 more processor system, then recon-all should complete >in about HALF the time as it usually does, since all the hemisphere > > > > > >specific stuff can be done in parallel. >At the completion of each hemipshere, it will email you. > >I included a command for each minute step so that people can easily > > > > > >fiddle with options and commands and so forth. > >Obviously, if you run recon-all -autoreon1, then you can then run >my script (after deleting the step1-??.done lines). >If you run recon-all -autorecon2, then you can run my script (after > > > > > >deleting the step1-??.done and step2-??.done lines) >And so forth. > >To see the script, go here: >http://www.nmr.mgh.harvard.edu/~daniel >click on fMRI scripts >click on super-recon > >Enjoy, and PLEASE email me if you use this. If there are >corrections I can easily post them. >Daniel > >>
Re: [Freesurfer] total intracranial volume question
Hi Eli, the eTIV is estimated from the talairach_with_skull.lta linear transform, so you might visually verify that it is correct on our subjects. chers, Bruce On Tue, 21 Mar 2006, Eli Diamond wrote: Hello, I'm writing because I am trying out some structure-function analyses and I would like to normalize my label volume measurements with the total intracranial volume. I was informed that this value is in /stats/aseg.stats. I was surprised at the range of TIVs that I saw in my 29 subjects (from 1400cm^3 to 2500cm^3). so I looked up what the normative values are for TIV, and it appears that the TIVs estimated for my group are irregular given the standard mean TIV and normal variance. (from one paper that I looked at it seems like the avereage TIV is around 1500cm^3 and that typical variation is measured in the 10-100cm^3 range, not an order of magnitude more than that.) Does anyone have any experience with the estimated TIV and what to expect as a normal range / how to know when something is wrong? Thanks so much! Best, Eli Diamond ___ 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] Faster and Parallel recon-all
Dhruman Thanks for catching that. Spelling was never my strong point. I have corrected the script on my website. As for you second problem, did you properly remove the waitfor step1-00.done from the motion correction step, since you say you skipped step1-00, i.e. the invol step? I mention this in a comment near the top of the script. D Goradia, Dhruman D wrote: Hi Daniel, I was having a second look at the script and apparently the script is fine with a small spelling error. The STAT variable which is set at 3 different instances has spelling error in "scripts" where "t" is missing. Once this was corrected the script is fine but it's still not working. It initiates all the processes and then just sits idle. After waiting for half an hour it still does not make step1-00.done (I start directly with motion cor) keeping all the other processes waiting. I am still probing into this. If you can think of something that might be of help then let me know. -Dhruman -Original Message- From: Daniel Goldenholz [mailto:[EMAIL PROTECTED] Sent: Tuesday 21 March 2006 11:25 To: Goradia, Dhruman D Subject: Re: [Freesurfer] Faster and Parallel recon-all Dhruman That's confusing. I think you should take one line of executable code from your script that produces that behavior and then email it to the freesurfer list. It sounds to me like the recon-all script ASSUMES that the log file exists if you specify a name. I thought it actually creates one first, but I could have been mistaken there, and if so I will need to add a few extra lines of code. PLEASE follow up on this. It will help others. The other thing to try is to create a text file first, such as like this: echo "#Starting recon-all manually..." > /Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.log and then see if my script is ok. Keep me posted. D Goradia, Dhruman D wrote: Hi Daniel, I tried to use the script super-recon on mac OX S using bash shell. I made the necessary changes to make it operable in bash. However when I run the script its gives me the following error: Tcsh:/Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.lo g :not a file or directory. I tried to run the first 3 steps of the script (motioncor, nuintensitycor, talairach) and it gives the above error. However if I remove the log and status flags, the first 3 steps executes properly. Do you have any idea why? Do you see any problem if I delete the log and status flags from the whole script and use it? -Dhruman -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Daniel Goldenholz Sent: Thursday 16 March 2006 15:17 Cc: Freesurfer Mailing List; Nick Schmansky Subject: Re: [Freesurfer] Faster and Parallel recon-all Ah. Silly me, I didn't notice the -log and -status options. Thanks Nick. I have now included those into my super-recon script as well. Problem solved. (if you have seen my script already, you may need to hit RELOAD on your browser to see the new version) Daniel Nick Schmansky wrote: The script looks good. The one thing it needs though is for the right and left hemi steps to log to separate files, otherwise output to recon- all.log will be interleaved, making debugging impossible. On Thu, 2006-03-16 at 12:15 -0500, Daniel Goldenholz wrote: Ooops. I sent the below with the wrong subject tag. Here it is again: Daniel Goldenholz wrote: Freesurfers I was hoping someone else would do this, but well, it seems that no one did. So I went ahead and made this myself. Amusingly, I don't NEED to reconstruct any brains right now, so I don't have anything to test this out with. Please someone try it, and let me know if it is helpful. What I did was write a script that runs each and every part of the recon-all -all stream, one command at a time. (based on the NEW version 3 stream). Each one is loaded with -waitfor and -notify so that the dependency structure is intact. However, ALL of the commands start running in the background! If you have a 2 more processor system, then recon-all should complete in about HALF the time as it usually does, since all the hemisphere specific stuff can be done in parallel. At the completion of each hemipshere, it will email you. I included a command for each minute step so that people can easily fiddle with options and commands and so forth. Obviously, if you run recon-all -autoreon1, then you can then run my script (after deleting the step1-??.done lines). If you run recon-all -autorecon2, then you can run my script (after deleting the step1-??.done and step2-??.done lines) And so forth. To see the script, go here
