Hello all,
I have some raw data and I'm not sure of the format. Its definitely not dicom. I ran recon-all on these files but I get an error saying it can't read the files. I have posted the output below. I tried to convert the files to afni format (BRIK + HEAD), and tried recon-all again. It ran for a while but gave an error that I've attached to a text file.
Can someone please tell me how I can get Freesurfer to read these files. I can also upload the raw files if you'd like to take a look at them.
Thanks a lot - Anil.
[root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid Nl-TA1-001 -sd /root/Freesurfer/Tone_Acquisition -all INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with -i, but -force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 76880 Feb 8 13:25 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-all.log Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux strings: Command not found. WM removal version /root/Freesurfer/Tone_Acquisition/Nl-TA1-001
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... genesisRead(): can't determine file name format for /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200
if you convert it to BRIK and visualize it does it look correct? On Thu, 8 Feb 2007, Anil Roy wrote:
Hello all,
I have some raw data and I'm not sure of the format. Its definitely not dicom. I ran recon-all on these files but I get an error saying it can't read the files. I have posted the output below. I tried to convert the files to afni format (BRIK + HEAD), and tried recon-all again. It ran for a while but gave an error that I've attached to a text file.
Can someone please tell me how I can get Freesurfer to read these files. I can also upload the raw files if you'd like to take a look at them.
Thanks a lot - Anil.
[root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid Nl-TA1-001 -sd /root/Freesurfer/Tone_Acquisition -all INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with -i, but -force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 76880 Feb 8 13:25 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-all.log Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux strings: Command not found. WM removal version /root/Freesurfer/Tone_Acquisition/Nl-TA1-001
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... genesisRead(): can't determine file name format for /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200
Yes. When I convert to BRIK and open with AFNI, the images show up fine in all three planes.
There is some noise towards the very end but it only shows up after the slices with no brain tissue (or any that I can see).
Anil.
On 2/8/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
if you convert it to BRIK and visualize it does it look correct? On Thu, 8 Feb 2007, Anil Roy wrote:
Hello all,
I have some raw data and I'm not sure of the format. Its definitely not dicom. I ran recon-all on these files but I get an error saying it can't read the files. I have posted the output below. I tried to convert the
files
to afni format (BRIK + HEAD), and tried recon-all again. It ran for a
while
but gave an error that I've attached to a text file.
Can someone please tell me how I can get Freesurfer to read these files.
I
can also upload the raw files if you'd like to take a look at them.
Thanks a lot - Anil.
[root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid Nl-TA1-001 -sd /root/Freesurfer/Tone_Acquisition -all INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with -i, but -force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 76880 Feb 8 13:25 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-all.log Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp#1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux strings: Command not found. WM removal version /root/Freesurfer/Tone_Acquisition/Nl-TA1-001
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... genesisRead(): can't determine file name format for /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp#1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200
I'll install the CentOS build and run the brain again.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com wrote:
Yes. When I convert to BRIK and open with AFNI, the images show up fine in all three planes.
There is some noise towards the very end but it only shows up after the slices with no brain tissue (or any that I can see).
Anil.
On 2/8/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
if you convert it to BRIK and visualize it does it look correct? On Thu, 8 Feb 2007, Anil Roy wrote:
Hello all,
I have some raw data and I'm not sure of the format. Its definitely
not
dicom. I ran recon-all on these files but I get an error saying it
can't
read the files. I have posted the output below. I tried to convert the
files
to afni format (BRIK + HEAD), and tried recon-all again. It ran for a
while
but gave an error that I've attached to a text file.
Can someone please tell me how I can get Freesurfer to read these
files. I
can also upload the raw files if you'd like to take a look at them.
Thanks a lot - Anil.
[root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid Nl-TA1-001
-sd
/root/Freesurfer/Tone_Acquisition -all INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with -i, but -force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 76880 Feb 8 13:25 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-all.log Linux dhcp-129-105-146-127.speech.northwestern.edu
2.6.17-1.2157_FC5smp #1
SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux strings: Command not found. WM removal version /root/Freesurfer/Tone_Acquisition/Nl-TA1-001
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... genesisRead(): can't determine file name format for /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 Linux dhcp-129-105-146-127.speech.northwestern.edu
2.6.17-1.2157_FC5smp #1
SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200
Hi All,
I installed the new build and Freesurfer still quits at the same place. I've attached the recon-all.log file to this email. Its still giving an error at the watershed step.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com wrote:
I'll install the CentOS build and run the brain again.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com wrote:
Yes. When I convert to BRIK and open with AFNI, the images show up fine in all three planes.
There is some noise towards the very end but it only shows up after the slices with no brain tissue (or any that I can see).
Anil.
On 2/8/07, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
if you convert it to BRIK and visualize it does it look correct? On Thu, 8 Feb 2007, Anil Roy wrote:
Hello all,
I have some raw data and I'm not sure of the format. Its definitely
not
dicom. I ran recon-all on these files but I get an error saying it
can't
read the files. I have posted the output below. I tried to convert
the files
to afni format (BRIK + HEAD), and tried recon-all again. It ran for
a while
but gave an error that I've attached to a text file.
Can someone please tell me how I can get Freesurfer to read these
files. I
can also upload the raw files if you'd like to take a look at them.
Thanks a lot - Anil.
[root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid Nl-TA1-001
-sd
/root/Freesurfer/Tone_Acquisition -all INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with -i,
but
-force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 76880 Feb 8 13:25 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-all.log Linux dhcp-129-105-146-127.speech.northwestern.edu
2.6.17-1.2157_FC5smp #1
SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux strings: Command not found. WM removal version /root/Freesurfer/Tone_Acquisition/Nl-TA1-001
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... genesisRead(): can't determine file name format for /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 Linux dhcp-129-105-146-127.speech.northwestern.edu
2.6.17-1.2157_FC5smp #1
SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200
did you check the talairach.xfm? On Thu, 8 Feb 2007, Anil Roy wrote:
Hi All,
I installed the new build and Freesurfer still quits at the same place. I've attached the recon-all.log file to this email. Its still giving an error at the watershed step.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com wrote:
I'll install the CentOS build and run the brain again.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com wrote:
Yes. When I convert to BRIK and open with AFNI, the images show up fine in all three planes.
There is some noise towards the very end but it only shows up after the slices with no brain tissue (or any that I can see).
Anil.
On 2/8/07, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
if you convert it to BRIK and visualize it does it look correct? On Thu, 8 Feb 2007, Anil Roy wrote:
Hello all,
I have some raw data and I'm not sure of the format. Its definitely
not
dicom. I ran recon-all on these files but I get an error saying it
can't
read the files. I have posted the output below. I tried to convert
the files
to afni format (BRIK + HEAD), and tried recon-all again. It ran for
a while
but gave an error that I've attached to a text file.
Can someone please tell me how I can get Freesurfer to read these
files. I
can also upload the raw files if you'd like to take a look at them.
Thanks a lot - Anil.
[root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid Nl-TA1-001
-sd
/root/Freesurfer/Tone_Acquisition -all INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with -i,
but
-force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 76880 Feb 8 13:25 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-all.log Linux dhcp-129-105-146-127.speech.northwestern.edu
2.6.17-1.2157_FC5smp #1
SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux strings: Command not found. WM removal version /root/Freesurfer/Tone_Acquisition/Nl-TA1-001
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... genesisRead(): can't determine file name format for /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 Linux dhcp-129-105-146-127.speech.northwestern.edu
2.6.17-1.2157_FC5smp #1
SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200
I've attached the talairach.xfm to this email. I'm a newbie to MRI analysis so I don't know what exactly would be a red flag in this file. Please do tell me if you see something odd.
Anil.
On 2/8/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
did you check the talairach.xfm? On Thu, 8 Feb 2007, Anil Roy wrote:
Hi All,
I installed the new build and Freesurfer still quits at the same place.
I've
attached the recon-all.log file to this email. Its still giving an error
at
the watershed step.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com wrote:
I'll install the CentOS build and run the brain again.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com wrote:
Yes. When I convert to BRIK and open with AFNI, the images show up
fine
in all three planes.
There is some noise towards the very end but it only shows up after
the
slices with no brain tissue (or any that I can see).
Anil.
On 2/8/07, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
if you convert it to BRIK and visualize it does it look correct? On Thu, 8 Feb 2007, Anil Roy wrote:
Hello all,
I have some raw data and I'm not sure of the format. Its
definitely
not
dicom. I ran recon-all on these files but I get an error saying
it
can't
read the files. I have posted the output below. I tried to
convert
the files
to afni format (BRIK + HEAD), and tried recon-all again. It ran
for
a while
but gave an error that I've attached to a text file.
Can someone please tell me how I can get Freesurfer to read these
files. I
can also upload the raw files if you'd like to take a look at
them.
Thanks a lot - Anil.
[root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid
Nl-TA1-001
-sd
/root/Freesurfer/Tone_Acquisition -all INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with
-i,
but
-force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 76880 Feb 8 13:25 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-
all.log
Linux dhcp-129-105-146-127.speech.northwestern.edu
2.6.17-1.2157_FC5smp #1
SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux strings: Command not found. WM removal version /root/Freesurfer/Tone_Acquisition/Nl-TA1-001
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... genesisRead(): can't determine file name format for /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 Linux dhcp-129-105-146-127.speech.northwestern.edu
2.6.17-1.2157_FC5smp #1
SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200
you need to visualize it in tkmedit. Use file -> load transform for main volume and see if it looks reasonable (should be slightly looking down, and pretty vertical so for example the interhemispheric fissure goes straight up and down in a coronal view On Thu, 8 Feb 2007, Anil Roy wrote:
I've attached the talairach.xfm to this email. I'm a newbie to MRI analysis so I don't know what exactly would be a red flag in this file. Please do tell me if you see something odd.
Anil.
On 2/8/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
did you check the talairach.xfm? On Thu, 8 Feb 2007, Anil Roy wrote:
Hi All,
I installed the new build and Freesurfer still quits at the same place.
I've
attached the recon-all.log file to this email. Its still giving an error
at
the watershed step.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com wrote:
I'll install the CentOS build and run the brain again.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com wrote:
Yes. When I convert to BRIK and open with AFNI, the images show up
fine
in all three planes.
There is some noise towards the very end but it only shows up after
the
slices with no brain tissue (or any that I can see).
Anil.
On 2/8/07, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
if you convert it to BRIK and visualize it does it look correct? On Thu, 8 Feb 2007, Anil Roy wrote:
> Hello all, > > I have some raw data and I'm not sure of the format. Its
definitely
not > dicom. I ran recon-all on these files but I get an error saying
it
can't > read the files. I have posted the output below. I tried to
convert
the files > to afni format (BRIK + HEAD), and tried recon-all again. It ran
for
a while > but gave an error that I've attached to a text file. > > Can someone please tell me how I can get Freesurfer to read these files. I > can also upload the raw files if you'd like to take a look at
them.
> > Thanks a lot - Anil. > > [root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i > /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid
Nl-TA1-001
-sd > /root/Freesurfer/Tone_Acquisition -all > INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition > INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with
-i,
but > -force specified. > Deleting any previous source volumes > Actual FREESURFER_HOME /usr/local/freesurfer > -rw-rw-r-- 1 root root 76880 Feb 8 13:25 > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-
all.log
> Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 > SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux > strings: Command not found. > WM removal version > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 > > mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz > > mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz > reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... > genesisRead(): can't determine file name format for > /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 > SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux > > recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200 >
Anil,
See this tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Also, a tool to appear in the next release, which checks the talairach.xfm against a known set of proper alignments, indicates that this alignment is bad. You probably will need to manually align.
Nick
On Thu, 2007-02-08 at 20:46 -0500, Bruce Fischl wrote:
you need to visualize it in tkmedit. Use file -> load transform for main volume and see if it looks reasonable (should be slightly looking down, and pretty vertical so for example the interhemispheric fissure goes straight up and down in a coronal view On Thu, 8 Feb 2007, Anil Roy wrote:
I've attached the talairach.xfm to this email. I'm a newbie to MRI analysis so I don't know what exactly would be a red flag in this file. Please do tell me if you see something odd.
Anil.
On 2/8/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
did you check the talairach.xfm? On Thu, 8 Feb 2007, Anil Roy wrote:
Hi All,
I installed the new build and Freesurfer still quits at the same place.
I've
attached the recon-all.log file to this email. Its still giving an error
at
the watershed step.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com wrote:
I'll install the CentOS build and run the brain again.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com wrote:
Yes. When I convert to BRIK and open with AFNI, the images show up
fine
in all three planes.
There is some noise towards the very end but it only shows up after
the
slices with no brain tissue (or any that I can see).
Anil.
On 2/8/07, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: > > if you convert it to BRIK and visualize it does it look correct? > On Thu, 8 > Feb 2007, Anil Roy wrote: > > > Hello all, > > > > I have some raw data and I'm not sure of the format. Its
definitely
> not > > dicom. I ran recon-all on these files but I get an error saying
it
> can't > > read the files. I have posted the output below. I tried to
convert
> the files > > to afni format (BRIK + HEAD), and tried recon-all again. It ran
for
> a while > > but gave an error that I've attached to a text file. > > > > Can someone please tell me how I can get Freesurfer to read these > files. I > > can also upload the raw files if you'd like to take a look at
them.
> > > > Thanks a lot - Anil. > > > > [root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i > > /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid
Nl-TA1-001
> -sd > > /root/Freesurfer/Tone_Acquisition -all > > INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition > > INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with
-i,
> but > > -force specified. > > Deleting any previous source volumes > > Actual FREESURFER_HOME /usr/local/freesurfer > > -rw-rw-r-- 1 root root 76880 Feb 8 13:25 > > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-
all.log
> > Linux dhcp-129-105-146-127.speech.northwestern.edu > 2.6.17-1.2157_FC5smp #1 > > SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux > > strings: Command not found. > > WM removal version > > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 > > > > mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz > > > > mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz > > reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... > > genesisRead(): can't determine file name format for > > /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > > Linux dhcp-129-105-146-127.speech.northwestern.edu > 2.6.17-1.2157_FC5smp #1 > > SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux > > > > recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200 > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think the first thing you should do is visualize your input in tkmedit to make sure it is oriented correctly. FreeSurfer and AFNI may be making different assumptions about the data.
doug
Nick Schmansky wrote:
Anil,
See this tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Also, a tool to appear in the next release, which checks the talairach.xfm against a known set of proper alignments, indicates that this alignment is bad. You probably will need to manually align.
Nick
On Thu, 2007-02-08 at 20:46 -0500, Bruce Fischl wrote:
you need to visualize it in tkmedit. Use file -> load transform for main volume and see if it looks reasonable (should be slightly looking down, and pretty vertical so for example the interhemispheric fissure goes straight up and down in a coronal view On Thu, 8 Feb 2007, Anil Roy wrote:
I've attached the talairach.xfm to this email. I'm a newbie to MRI analysis so I don't know what exactly would be a red flag in this file. Please do tell me if you see something odd.
Anil.
On 2/8/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
did you check the talairach.xfm? On Thu, 8 Feb 2007, Anil Roy wrote:
Hi All,
I installed the new build and Freesurfer still quits at the same place.
I've
attached the recon-all.log file to this email. Its still giving an error
at
the watershed step.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com wrote:
I'll install the CentOS build and run the brain again.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com wrote:
>Yes. When I convert to BRIK and open with AFNI, the images show up > >
fine
>in all three planes. > >There is some noise towards the very end but it only shows up after > >
the
>slices with no brain tissue (or any that I can see). > >Anil. > >On 2/8/07, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: > > >>if you convert it to BRIK and visualize it does it look correct? >>On Thu, 8 >>Feb 2007, Anil Roy wrote: >> >> >> >>>Hello all, >>> >>>I have some raw data and I'm not sure of the format. Its >>> >>>
definitely
>>not >> >> >>>dicom. I ran recon-all on these files but I get an error saying >>> >>>
it
>>can't >> >> >>>read the files. I have posted the output below. I tried to >>> >>>
convert
>>the files >> >> >>>to afni format (BRIK + HEAD), and tried recon-all again. It ran >>> >>>
for
>>a while >> >> >>>but gave an error that I've attached to a text file. >>> >>>Can someone please tell me how I can get Freesurfer to read these >>> >>> >>files. I >> >> >>>can also upload the raw files if you'd like to take a look at >>> >>>
them.
>>>Thanks a lot - Anil. >>> >>>[root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i >>>/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid >>> >>>
Nl-TA1-001
>>-sd >> >> >>>/root/Freesurfer/Tone_Acquisition -all >>>INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition >>>INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with >>> >>>
-i,
>>but >> >> >>>-force specified. >>>Deleting any previous source volumes >>>Actual FREESURFER_HOME /usr/local/freesurfer >>>-rw-rw-r-- 1 root root 76880 Feb 8 13:25 >>>/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon- >>> >>>
all.log
>>>Linux dhcp-129-105-146-127.speech.northwestern.edu >>> >>> >>2.6.17-1.2157_FC5smp #1 >> >> >>>SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux >>>strings: Command not found. >>>WM removal version >>>/root/Freesurfer/Tone_Acquisition/Nl-TA1-001 >>> >>>mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 >>>/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz >>> >>>mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 >>>/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz >>>reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... >>>genesisRead(): can't determine file name format for >>>/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 >>>Linux dhcp-129-105-146-127.speech.northwestern.edu >>> >>> >>2.6.17-1.2157_FC5smp #1 >> >> >>>SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux >>> >>>recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200 >>> >>> >>> > >
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
Thanks a lot for all your input. I will check out the xfm in tkmedit and get back to you with the results.
Anil.
On 2/9/07, Doug Greve greve@nmr.mgh.harvard.edu wrote:
I think the first thing you should do is visualize your input in tkmedit to make sure it is oriented correctly. FreeSurfer and AFNI may be making different assumptions about the data.
doug
Nick Schmansky wrote:
Anil,
See this tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Also, a tool to appear in the next release, which checks thetalairach.xfm against a known set of proper alignments, indicates that this alignment is bad. You probably will need to manually align.
Nick
On Thu, 2007-02-08 at 20:46 -0500, Bruce Fischl wrote:
you need to visualize it in tkmedit. Use file -> load transform for main volume and see if it looks reasonable (should be slightly looking down, and pretty vertical so for example the interhemispheric fissure goes straight up and down in a coronal view On Thu, 8 Feb 2007, Anil Roy wrote:
I've attached the talairach.xfm to this email. I'm a newbie to MRI analysisso I don't know what exactly would be a red flag in this file. Please do tell me if you see something odd.
Anil.
On 2/8/07, Bruce Fischl fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu wrote:
did you check the talairach.xfm? On Thu, 8 Feb 2007, Anil Roy wrote:
Hi All,I installed the new build and Freesurfer still quits at the same place.
I've
attached the recon-all.log file to this email. Its still giving an error
at
the watershed step.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com aroy85@gmail.com wrote:
I'll install the CentOS build and run the brain again.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com aroy85@gmail.com wrote:
Yes. When I convert to BRIK and open with AFNI, the images show up
fine
in all three planes.
There is some noise towards the very end but it only shows up after
the
slices with no brain tissue (or any that I can see).
Anil.
On 2/8/07, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
if you convert it to BRIK and visualize it does it look correct? On Thu, 8 Feb 2007, Anil Roy wrote:
Hello all,I have some raw data and I'm not sure of the format. Its
definitely
not
dicom. I ran recon-all on these files but I get an error saying
it
can't
read the files. I have posted the output below. I tried to
convert
the files
to afni format (BRIK + HEAD), and tried recon-all again. It ran
for
a while
but gave an error that I've attached to a text file.
Can someone please tell me how I can get Freesurfer to read these
files. I
can also upload the raw files if you'd like to take a look at
them.
Thanks a lot - Anil.
[root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid
Nl-TA1-001
-sd
/root/Freesurfer/Tone_Acquisition -all INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with
-i,
but
-force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 76880 Feb 8 13:25 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-
all.log
Linux dhcp-129-105-146-127.speech.northwestern.edu
2.6.17-1.2157_FC5smp #1
SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux strings: Command not found. WM removal version /root/Freesurfer/Tone_Acquisition/Nl-TA1-001
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... genesisRead(): can't determine file name format for /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 Linux dhcp-129-105-146-127.speech.northwestern.edu
2.6.17-1.2157_FC5smp #1
SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200
_______________________________________________Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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
Hi Anil,
my suggestion was to first look at the volume in tkmedit without the xfm, then, if that is oriented correctly and looks ok, move on to the xfm
doug
Anil Roy wrote:
Thanks a lot for all your input. I will check out the xfm in tkmedit and get back to you with the results.
Anil.
On 2/9/07, Doug Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think the first thing you should do is visualize your input in tkmedit to make sure it is oriented correctly. FreeSurfer and AFNI may be making different assumptions about the data. doug Nick Schmansky wrote:Anil,
See this tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Also, a tool to appear in the next release, which checks the talairach.xfm against a known set of proper alignments, indicates that this alignment is bad. You probably will need to manually align.
Nick
On Thu, 2007-02-08 at 20:46 -0500, Bruce Fischl wrote:
you need to visualize it in tkmedit. Use file -> load transform for main volume and see if it looks reasonable (should be slightly looking down, and pretty vertical so for example the interhemispheric fissure goes
straight up and down in a coronal view On Thu, 8 Feb 2007, Anil Roy wrote:
I've attached the talairach.xfm to this email. I'm a newbie to MRI analysis so I don't know what exactly would be a red flag in this file. Please do tell me if you see something odd.
Anil.
On 2/8/07, Bruce Fischl fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu wrote:
did you check the talairach.xfm? On Thu, 8 Feb 2007, Anil Roy wrote:
Hi All,
I installed the new build and Freesurfer still quits at the same place.
I've
attached the recon-all.log file to this email. Its still giving an error
at
the watershed step.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com mailto:aroy85@gmail.com wrote:
>I'll install the CentOS build and run the brain again. > >Anil. > >On 2/8/07, Anil Roy >aroy85@gmail.com mailto:aroy85@gmail.com wrote: > > >>Yes. When I convert to BRIK and open with AFNI, the images show up >> >>
fine
>>in all three planes. >> >>There is some noise towards the very end but it only shows up after >> >>
the
>>slices with no brain tissue (or any that I can see). >> >>Anil. >> >>On 2/8/07, Bruce Fischl < >>fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: >> >> >>>if you convert it to BRIK and visualize it does it look correct? >>>On Thu, 8 >>>Feb 2007, Anil Roy wrote: >>> >>> >>> >>>>Hello all, >>>> >>>>I have some raw data and I'm not sure of the format. Its >>>> >>>>
definitely
>>>not >>> >>> >>>>dicom. I ran recon-all on these files but I get an error saying >>>> >>>>
it
>>>can't >>> >>> >>>>read the files. I have posted the output below. I tried to >>>> >>>>
convert
>>>the files >>> >>> >>>>to afni format (BRIK + HEAD), and tried recon-all again. It ran >>>> >>>>
for
>>>a while >>> >>> >>>>but gave an error that I've attached to a text file. >>>> >>>>Can someone please tell me how I can get Freesurfer to read these >>>> >>>> >>>files. I >>> >>> >>>>can also upload the raw files if you'd like to take a look at >>>> >>>>
them.
>>>>Thanks a lot - Anil. >>>> >>>>[root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i >>>>/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid >>>> >>>>
Nl-TA1-001
>>>-sd >>> >>> >>>>/root/Freesurfer/Tone_Acquisition -all >>>>INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition >>>>INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with >>>> >>>>
-i,
>>>but >>> >>> >>>>-force specified. >>>>Deleting any previous source volumes >>>>Actual FREESURFER_HOME /usr/local/freesurfer >>>>-rw-rw-r-- 1 root root 76880 Feb 8 13:25 >>>>/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon- >>>> >>>> >>>>
all.log
>>>>Linux dhcp-129-105-146-127.speech.northwestern.edu http://dhcp-129-105-146-127.speech.northwestern.edu >>>> >>>> >>>2.6.17-1.2157_FC5smp #1 >>> >>> >>>>SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux >>>>strings: Command not found. >>>>WM removal version >>>>/root/Freesurfer/Tone_Acquisition/Nl-TA1-001 >>>> >>>>mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 >>>> >>>>/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz >>>> >>>>mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 >>>>/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz >>>>reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... >>>> >>>>genesisRead(): can't determine file name format for >>>>/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 >>>>Linux >>>>dhcp-129-105-146-127.speech.northwestern.edu http://dhcp-129-105-146-127.speech.northwestern.edu >>>> >>>> >>>2.6.17-1.2157_FC5smp #1 >>> >>> >>>>SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux >>>> >>>>recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200 >>>> >>>> >>>> >> >>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I loaded up the orig volumes and the xfm. The brainmask volume isn't there because freesurfer quit at the skull strip phase. I've attached the tiffs of the orig and xfm to this email. As you'll see, the xfm does look quite bad. Do you know how I could correct this.
The manual mentions using tkregister2, but when I run it I get an error(also attached) because the surfaces weren't generated. Is there a different way to use tkregister2 to correct the output.
Thanks,
Anil
On 2/9/07, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Hi Anil,
my suggestion was to first look at the volume in tkmedit without the xfm, then, if that is oriented correctly and looks ok, move on to the xfm
doug
Anil Roy wrote:
Thanks a lot for all your input. I will check out the xfm in tkmedit and get back to you with the results.
Anil.
On 2/9/07, Doug Greve < greve@nmr.mgh.harvard.edu> wrote:
I think the first thing you should do is visualize your input in tkmedit to make sure it is oriented correctly. FreeSurfer and AFNI may be making different assumptions about the data.
doug
Nick Schmansky wrote:
Anil,
See this tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Also, a tool to appear in the next release, which checks thetalairach.xfm against a known set of proper alignments, indicates that this alignment is bad. You probably will need to manually align.
Nick
On Thu, 2007-02-08 at 20:46 -0500, Bruce Fischl wrote:
you need to visualize it in tkmedit. Use file -> load transform for main volume and see if it looks reasonable (should be slightly looking down, and pretty vertical so for example the interhemispheric fissure goes
straight up and down in a coronal view On Thu, 8 Feb 2007, Anil Roy wrote:
I've attached the talairach.xfm to this email. I'm a newbie to MRI analysisso I don't know what exactly would be a red flag in this file. Please do tell me if you see something odd.
Anil.
On 2/8/07, Bruce Fischl fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu wrote:
did you check the talairach.xfm? On Thu, 8 Feb 2007, Anil Roy wrote:
Hi All,I installed the new build and Freesurfer still quits at the same place.
I've
attached the recon-all.log file to this email. Its still giving an error
at
the watershed step.
Anil.
On 2/8/07, Anil Roy aroy85@gmail.com aroy85@gmail.com wrote:
I'll install the CentOS build and run the brain again.Anil.
On 2/8/07, Anil Roy aroy85@gmail.com aroy85@gmail.com wrote:
Yes. When I convert to BRIK and open with AFNI, the images show up
fine
in all three planes.
There is some noise towards the very end but it only shows up after
the
slices with no brain tissue (or any that I can see).
Anil.
On 2/8/07, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
if you convert it to BRIK and visualize it does it look correct? On Thu, 8 Feb 2007, Anil Roy wrote:
Hello all,I have some raw data and I'm not sure of the format. Its
definitely
not
dicom. I ran recon-all on these files but I get an error saying
it
can't
read the files. I have posted the output below. I tried to
convert
the files
to afni format (BRIK + HEAD), and tried recon-all again. It ran
for
a while
but gave an error that I've attached to a text file.
Can someone please tell me how I can get Freesurfer to read these
files. I
can also upload the raw files if you'd like to take a look at
them.
Thanks a lot - Anil.
[root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid
Nl-TA1-001
-sd
/root/Freesurfer/Tone_Acquisition -all INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with
-i,
but
-force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 76880 Feb 8 13:25 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-
all.logLinux dhcp-129-105-146-127.speech.northwestern.edu
2.6.17-1.2157_FC5smp #1
SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux strings: Command not found. WM removal version /root/Freesurfer/Tone_Acquisition/Nl-TA1-001
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001
/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz
mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001...
genesisRead(): can't determine file name format for /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 Linux dhcp-129-105-146-127.speech.northwestern.edu
2.6.17-1.2157_FC5smp #1
SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200
_______________________________________________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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu
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.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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
Anil,
exclude the argument '--surf orig' from tkregister2 if the surfaces are not available.
Nick
On Mon, 2007-02-12 at 16:58 -0600, Anil Roy wrote:
Hi,
I loaded up the orig volumes and the xfm. The brainmask volume isn't there because freesurfer quit at the skull strip phase. I've attached the tiffs of the orig and xfm to this email. As you'll see, the xfm does look quite bad. Do you know how I could correct this.
The manual mentions using tkregister2, but when I run it I get an error(also attached) because the surfaces weren't generated. Is there a different way to use tkregister2 to correct the output.
Thanks,
Anil
On 2/9/07, Doug Greve greve@nmr.mgh.harvard.edu wrote: Hi Anil,
my suggestion was to first look at the volume in tkmedit without the xfm, then, if that is oriented correctly and looks ok, move on to the xfm doug Anil Roy wrote: > Thanks a lot for all your input. I will check out the xfm in > tkmedit and get back to you with the results. > > Anil. > > On 2/9/07, Doug Greve <greve@nmr.mgh.harvard.edu> wrote: > I think the first thing you should do is visualize > your input in tkmedit to make sure it is oriented > correctly. FreeSurfer and AFNI may be making > different assumptions about the data. > > doug > > > Nick Schmansky wrote: > > Anil, > > > > See this tutorial: > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > > > > > > > Also, a tool to appear in the next release, which checks the > > talairach.xfm against a known set of proper alignments, indicates that > > this alignment is bad. You probably will need to manually align. > > > > Nick > > > > On Thu, 2007-02-08 at 20:46 -0500, Bruce Fischl wrote: > > > > > you need to visualize it in tkmedit. Use file -> load transform for main > > > volume and see if it looks reasonable (should be slightly looking down, > > > and pretty vertical so for example the interhemispheric fissure goes > > > > > > > > > straight up and down in a coronal view > > > On Thu, 8 Feb 2007, Anil Roy wrote: > > > > > > > > > > I've attached the talairach.xfm to this email. I'm a newbie to MRI analysis > > > > so I don't know what exactly would be a red flag in this file. Please do > > > > tell me if you see something odd. > > > > > > > > > > > > Anil. > > > > > > > > > > > > On 2/8/07, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > > > > > > > > > did you check the talairach.xfm? > > > > > On Thu, 8 Feb 2007, Anil Roy wrote: > > > > > > > > > > > > > > > > Hi All, > > > > > > > > > > > > I installed the new build and Freesurfer still quits at the same place. > > > > > > > > > > > I've > > > > > > > > > > > attached the recon-all.log file to this email. Its still giving an error > > > > > > > > > > > at > > > > > > > > > > > the watershed step. > > > > > > > > > > > > Anil. > > > > > > > > > > > > On 2/8/07, Anil Roy <aroy85@gmail.com> wrote: > > > > > > > > > > > > > > > > > > > > > > > > > I'll install the CentOS build and run the brain again. > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > On 2/8/07, Anil Roy > > > > > > > > > > > > > > <aroy85@gmail.com> wrote: > > > > > > > > > > > > > > > Yes. When I convert to BRIK and open with AFNI, the images show up > > > > > > > > > > > > > fine > > > > > > > > > > > > > in all three planes. > > > > > > > > > > > > > > > > There is some noise towards the very end but it only shows up after > > > > > > > > > > > > > the > > > > > > > > > > > > > slices with no brain tissue (or any that I can see). > > > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > > > On 2/8/07, Bruce Fischl < > > > > > > > > > > > > > > > > fischl@nmr.mgh.harvard.edu> wrote: > > > > > > > > > > > > > > > > > if you convert it to BRIK and visualize it does it look correct? > > > > > > > > > On Thu, 8 > > > > > > > > > Feb 2007, Anil Roy wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > Hello all, > > > > > > > > > > > > > > > > > > > > I have some raw data and I'm not sure of the format. Its > > > > > > > > > > > > > > > definitely > > > > > > > > > > > > > > not > > > > > > > > > > > > > > > > > > > dicom. I ran recon-all on these files but I get an error saying > > > > > > > > > > > > > > > it > > > > > > > > > > > > > > can't > > > > > > > > > > > > > > > > > > > read the files. I have posted the output below. I tried to > > > > > > > > > > > > > > > convert > > > > > > > > > > > > > > the files > > > > > > > > > > > > > > > > > > > to afni format (BRIK + HEAD), and tried recon-all again. It ran > > > > > > > > > > > > > > > for > > > > > > > > > > > > > > a while > > > > > > > > > > > > > > > > > > > but gave an error that I've attached to a text file. > > > > > > > > > > > > > > > > > > > > Can someone please tell me how I can get Freesurfer to read these > > > > > > > > > > > > > > > > > > > files. I > > > > > > > > > > > > > > > > > > > can also upload the raw files if you'd like to take a look at > > > > > > > > > > > > > > > them. > > > > > > > > > > > > > > > Thanks a lot - Anil. > > > > > > > > > > > > > > > > > > > > [root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i > > > > > > > > > > /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid > > > > > > > > > > > > > > > Nl-TA1-001 > > > > > > > > > > > > > > -sd > > > > > > > > > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition -all > > > > > > > > > > INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition > > > > > > > > > > INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with > > > > > > > > > > > > > > > -i, > > > > > > > > > > > > > > but > > > > > > > > > > > > > > > > > > > -force specified. > > > > > > > > > > Deleting any previous source volumes > > > > > > > > > > Actual FREESURFER_HOME /usr/local/freesurfer > > > > > > > > > > -rw-rw-r-- 1 root root 76880 Feb 8 13:25 > > > > > > > > > > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon- > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > all.log > > > > > > > > > > > > > > > Linux dhcp-129-105-146-127.speech.northwestern.edu > > > > > > > > > > > > > > > > > > > 2.6.17-1.2157_FC5smp #1 > > > > > > > > > > > > > > > > > > > SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux > > > > > > > > > > strings: Command not found. > > > > > > > > > > WM removal version > > > > > > > > > > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 > > > > > > > > > > > > > > > > > > > > mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz > > > > > > > > > > > > > > > > > > > > mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > > > > > > > > > > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz > > > > > > > > > > reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > genesisRead(): can't determine file name format for > > > > > > > > > > /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > > > > > > > > > > Linux > > > > > > > > > > > > > > > > > > > > dhcp-129-105-146-127.speech.northwestern.edu > > > > > > > > > > > > > > > > > > > 2.6.17-1.2157_FC5smp #1 > > > > > > > > > > > > > > > > > > > SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux > > > > > > > > > > > > > > > > > > > > recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > 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 > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > > 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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
Hi All,
I followed the steps in the tutorial on tkregister2 to align the two volumes and saved the new reg. Following this I ran recon-all again but freesurfer still quits at the watershed step. I've attached a file with the output to this email. Do you know if something else could be causing the problem.
Thanks a lot,
Anil.
On 2/12/07, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Anil,
exclude the argument '--surf orig' from tkregister2 if the surfaces are not available.
Nick
On Mon, 2007-02-12 at 16:58 -0600, Anil Roy wrote:
Hi,
I loaded up the orig volumes and the xfm. The brainmask volume isn't there because freesurfer quit at the skull strip phase. I've attached the tiffs of the orig and xfm to this email. As you'll see, the xfm does look quite bad. Do you know how I could correct this.
The manual mentions using tkregister2, but when I run it I get an error(also attached) because the surfaces weren't generated. Is there a different way to use tkregister2 to correct the output.
Thanks,
Anil
On 2/9/07, Doug Greve greve@nmr.mgh.harvard.edu wrote: Hi Anil,
my suggestion was to first look at the volume in tkmedit without the xfm, then, if that is oriented correctly and looks ok, move on to the xfm doug Anil Roy wrote: > Thanks a lot for all your input. I will check out the xfm in > tkmedit and get back to you with the results. > > Anil. > > On 2/9/07, Doug Greve <greve@nmr.mgh.harvard.edu> wrote: > I think the first thing you should do is visualize > your input in tkmedit to make sure it is oriented > correctly. FreeSurfer and AFNI may be making > different assumptions about the data. > > doug > > > Nick Schmansky wrote: > > Anil, > > > > See this tutorial: > > > >https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
> > > > > > > > Also, a tool to appear in the next release, whichchecks the
> > talairach.xfm against a known set of properalignments, indicates that
> > this alignment is bad. You probably will need tomanually align.
> > > > Nick > > > > On Thu, 2007-02-08 at 20:46 -0500, Bruce Fischlwrote:
> > > > > you need to visualize it in tkmedit. Use file ->load transform for main
> > > volume and see if it looks reasonable (should beslightly looking down,
> > > and pretty vertical so for example theinterhemispheric fissure goes
> > > > > > > > > straight up and down in a coronal view > > > On Thu, 8 Feb 2007, Anil Roy wrote: > > > > > > > > > > I've attached the talairach.xfm to this email.I'm a newbie to MRI analysis
> > > > so I don't know what exactly would be a red flagin this file. Please do
> > > > tell me if you see something odd. > > > > > > > > > > > > Anil. > > > > > > > > > > > > On 2/8/07, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> > > > > > > > > did you check the talairach.xfm? > > > > > On Thu, 8 Feb 2007, Anil Roy wrote: > > > > > > > > > > > > > > > > Hi All, > > > > > > > > > > > > I installed the new build and Freesurferstill quits at the same place.
> > > > > > > > > > > I've > > > > > > > > > > > attached the recon-all.log file to thisemail. Its still giving an error
> > > > > > > > > > > at > > > > > > > > > > > the watershed step. > > > > > > > > > > > > Anil. > > > > > > > > > > > > On 2/8/07, Anil Roy <aroy85@gmail.com>wrote:
> > > > > > > > > > > > > > > > > > > > > > > > > I'll install the CentOS build and run thebrain again.
> > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > On 2/8/07, Anil Roy > > > > > > > > > > > > > > <aroy85@gmail.com> wrote: > > > > > > > > > > > > > > > Yes. When I convert to BRIK and openwith AFNI, the images show up
> > > > > > > > > > > > > fine > > > > > > > > > > > > > in all three planes. > > > > > > > > > > > > > > > > There is some noise towards the very endbut it only shows up after
> > > > > > > > > > > > > the > > > > > > > > > > > > > slices with no brain tissue (or any thatI can see).
> > > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > > > On 2/8/07, Bruce Fischl < > > > > > > > > > > > > > > > > fischl@nmr.mgh.harvard.edu> wrote: > > > > > > > > > > > > > > > > > if you convert it to BRIK andvisualize it does it look correct?
> > > > > > > > > On Thu, 8 > > > > > > > > > Feb 2007, Anil Roy wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > Hello all, > > > > > > > > > > > > > > > > > > > > I have some raw data and I'm notsure of the format. Its
> > > > > > > > > > > > > > > definitely > > > > > > > > > > > > > > not > > > > > > > > > > > > > > > > > > > dicom. I ran recon-all on thesefiles but I get an error saying
> > > > > > > > > > > > > > > it > > > > > > > > > > > > > > can't > > > > > > > > > > > > > > > > > > > read the files. I have posted theoutput below. I tried to
> > > > > > > > > > > > > > > convert > > > > > > > > > > > > > > the files > > > > > > > > > > > > > > > > > > > to afni format (BRIK + HEAD), andtried recon-all again. It ran
> > > > > > > > > > > > > > > for > > > > > > > > > > > > > > a while > > > > > > > > > > > > > > > > > > > but gave an error that I've attachedto a text file.
> > > > > > > > > > > > > > > > > > > > Can someone please tell me how I canget Freesurfer to read these
> > > > > > > > > > > > > > > > > > > files. I > > > > > > > > > > > > > > > > > > > can also upload the raw files ifyou'd like to take a look at
> > > > > > > > > > > > > > > them. > > > > > > > > > > > > > > > Thanks a lot - Anil. > > > > > > > > > > > > > > > > > > > > [root@dhcp-129-105-146-127freesurfer]# recon-all -force -i > > > > > > > > > >/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid
> > > > > > > > > > > > > > > Nl-TA1-001 > > > > > > > > > > > > > > -sd > > > > > > > > > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition-all
> > > > > > > > > > INFO: SUBJECTS_DIR is/root/Freesurfer/Tone_Acquisition
> > > > > > > > > > INFO:/root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with
> > > > > > > > > > > > > > > -i, > > > > > > > > > > > > > > but > > > > > > > > > > > > > > > > > > > -force specified. > > > > > > > > > > Deleting any previous source volumes > > > > > > > > > > Actual FREESURFER_HOME/usr/local/freesurfer
> > > > > > > > > > -rw-rw-r-- 1 root root 76880 Feb 813:25
> > > > > > > > > >/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-
> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > all.log > > > > > > > > > > > > > > > Linuxdhcp-129-105-146-127.speech.northwestern.edu
> > > > > > > > > > > > > > > > > > > 2.6.17-1.2157_FC5smp #1 > > > > > > > > > > > > > > > > > > > SMP Tue Jul 11 23:24:16 EDT 2006i686 i686 i386 GNU/Linux
> > > > > > > > > > strings: Command not found. > > > > > > > > > > WM removal version > > > > > > > > > >/root/Freesurfer/Tone_Acquisition/Nl-TA1-001
> > > > > > > > > > > > > > > > > > > > mri_convert/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001
> > > > > > > > > > > > > > > > > > > > > > > > > > > > > >/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz
> > > > > > > > > > > > > > > > > > > > mri_convert/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001
> > > > > > > > > >/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz
> > > > > > > > > > reading from/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001...
> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > genesisRead(): can't determine filename format for
> > > > > > > > > >/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001
> > > > > > > > > > Linux > > > > > > > > > > > > > > > > > > > >dhcp-129-105-146-127.speech.northwestern.edu
> > > > > > > > > > > > > > > > > > > 2.6.17-1.2157_FC5smp #1 > > > > > > > > > > > > > > > > > > > SMP Tue Jul 11 23:24:16 EDT 2006i686 i686 i386 GNU/Linux
> > > > > > > > > > > > > > > > > > > > recon-all exited with ERRORS at ThuFeb 8 13:52:57 CST 200
> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > 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
> > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the stepsin:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > ____________________________________________________________ > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu 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
Anil,
Can you send me the orig.mgz file? You can upload it to my email address via:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Nick
On Wed, 2007-02-14 at 14:54 -0600, Anil Roy wrote:
Hi All,
I followed the steps in the tutorial on tkregister2 to align the two volumes and saved the new reg. Following this I ran recon-all again but freesurfer still quits at the watershed step. I've attached a file with the output to this email. Do you know if something else could be causing the problem.
Thanks a lot,
Anil.
On 2/12/07, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: Anil,
exclude the argument '--surf orig' from tkregister2 if the surfaces are not available. Nick On Mon, 2007-02-12 at 16:58 -0600, Anil Roy wrote: > Hi, > > I loaded up the orig volumes and the xfm. The brainmask volume isn't > there because freesurfer quit at the skull strip phase. I've attached > the tiffs of the orig and xfm to this email. As you'll see, the xfm > does look quite bad. Do you know how I could correct this. > > The manual mentions using tkregister2, but when I run it I get an > error(also attached) because the surfaces weren't generated. Is there > a different way to use tkregister2 to correct the output. > > Thanks, > > Anil > > On 2/9/07, Doug Greve < greve@nmr.mgh.harvard.edu> wrote: > Hi Anil, > > my suggestion was to first look at the volume in tkmedit > without the xfm, then, if that is oriented correctly and looks > ok, move on to the xfm > > doug > > Anil Roy wrote: > > Thanks a lot for all your input. I will check out the xfm in > > tkmedit and get back to you with the results. > > > > Anil. > > > > On 2/9/07, Doug Greve <greve@nmr.mgh.harvard.edu> wrote: > > I think the first thing you should do is visualize > > your input in tkmedit to make sure it is oriented > > correctly. FreeSurfer and AFNI may be making > > different assumptions about the data. > > > > doug > > > > > > Nick Schmansky wrote: > > > Anil, > > > > > > See this tutorial: > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > > > > > > > > > > > Also, a tool to appear in the next release, which checks the > > > talairach.xfm against a known set of proper alignments, indicates that > > > this alignment is bad. You probably will need to manually align. > > > > > > Nick > > > > > > On Thu, 2007-02-08 at 20:46 -0500, Bruce Fischl wrote: > > > > > > > you need to visualize it in tkmedit. Use file -> load transform for main > > > > volume and see if it looks reasonable (should be slightly looking down, > > > > and pretty vertical so for example the interhemispheric fissure goes > > > > > > > > > > > > straight up and down in a coronal view > > > > On Thu, 8 Feb 2007, Anil Roy wrote: > > > > > > > > > > > > > I've attached the talairach.xfm to this email. I'm a newbie to MRI analysis > > > > > so I don't know what exactly would be a red flag in this file. Please do > > > > > tell me if you see something odd. > > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > > On 2/8/07, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > > > > > > > > > > > did you check the talairach.xfm? > > > > > > On Thu, 8 Feb 2007, Anil Roy wrote: > > > > > > > > > > > > > > > > > > > Hi All, > > > > > > > > > > > > > > I installed the new build and Freesurfer still quits at the same place. > > > > > > > > > > > > > I've > > > > > > > > > > > > > attached the recon-all.log file to this email. Its still giving an error > > > > > > > > > > > > > at > > > > > > > > > > > > > the watershed step. > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > On 2/8/07, Anil Roy < aroy85@gmail.com> wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > I'll install the CentOS build and run the brain again. > > > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > > > On 2/8/07, Anil Roy > > > > > > > > > > > > > > > > < aroy85@gmail.com> wrote: > > > > > > > > > > > > > > > > > Yes. When I convert to BRIK and open with AFNI, the images show up > > > > > > > > > > > > > > > fine > > > > > > > > > > > > > > > in all three planes. > > > > > > > > > > > > > > > > > > There is some noise towards the very end but it only shows up after > > > > > > > > > > > > > > > the > > > > > > > > > > > > > > > slices with no brain tissue (or any that I can see). > > > > > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > > > > > On 2/8/07, Bruce Fischl < > > > > > > > > > > > > > > > > > > fischl@nmr.mgh.harvard.edu> wrote: > > > > > > > > > > > > > > > > > > > if you convert it to BRIK and visualize it does it look correct? > > > > > > > > > > On Thu, 8 > > > > > > > > > > Feb 2007, Anil Roy wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Hello all, > > > > > > > > > > > > > > > > > > > > > > I have some raw data and I'm not sure of the format. Its > > > > > > > > > > > > > > > > > definitely > > > > > > > > > > > > > > > > not > > > > > > > > > > > > > > > > > > > > > dicom. I ran recon-all on these files but I get an error saying > > > > > > > > > > > > > > > > > it > > > > > > > > > > > > > > > > can't > > > > > > > > > > > > > > > > > > > > > read the files. I have posted the output below. I tried to > > > > > > > > > > > > > > > > > convert > > > > > > > > > > > > > > > > the files > > > > > > > > > > > > > > > > > > > > > to afni format (BRIK + HEAD), and tried recon-all again. It ran > > > > > > > > > > > > > > > > > for > > > > > > > > > > > > > > > > a while > > > > > > > > > > > > > > > > > > > > > but gave an error that I've attached to a text file. > > > > > > > > > > > > > > > > > > > > > > Can someone please tell me how I can get Freesurfer to read these > > > > > > > > > > > > > > > > > > > > > files. I > > > > > > > > > > > > > > > > > > > > > can also upload the raw files if you'd like to take a look at > > > > > > > > > > > > > > > > > them. > > > > > > > > > > > > > > > > > Thanks a lot - Anil. > > > > > > > > > > > > > > > > > > > > > > [root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i > > > > > > > > > > > /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid > > > > > > > > > > > > > > > > > Nl-TA1-001 > > > > > > > > > > > > > > > > -sd > > > > > > > > > > > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition -all > > > > > > > > > > > INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition > > > > > > > > > > > INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with > > > > > > > > > > > > > > > > > -i, > > > > > > > > > > > > > > > > but > > > > > > > > > > > > > > > > > > > > > -force specified. > > > > > > > > > > > Deleting any previous source volumes > > > > > > > > > > > Actual FREESURFER_HOME /usr/local/freesurfer > > > > > > > > > > > -rw-rw-r-- 1 root root 76880 Feb 8 13:25 > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon- > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > all.log > > > > > > > > > > > > > > > > > Linux dhcp-129-105-146-127.speech.northwestern.edu > > > > > > > > > > > > > > > > > > > > > 2.6.17-1.2157_FC5smp #1 > > > > > > > > > > > > > > > > > > > > > SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux > > > > > > > > > > > strings: Command not found. > > > > > > > > > > > WM removal version > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 > > > > > > > > > > > > > > > > > > > > > > mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition/Nl- TA1-001/mri/orig/001.mgz > > > > > > > > > > > > > > > > > > > > > > mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition/Nl- TA1-001/mri/orig/001.mgz > > > > > > > > > > > reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > genesisRead(): can't determine file name format for > > > > > > > > > > > /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > > > > > > > > > > > Linux > > > > > > > > > > > > > > > > > > > > > > dhcp-129-105-146-127.speech.northwestern.edu > > > > > > > > > > > > > > > > > > > > > 2.6.17-1.2157_FC5smp #1 > > > > > > > > > > > > > > > > > > > > > SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux > > > > > > > > > > > > > > > > > > > > > > recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > 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 > > > > > > > > > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu > > > > 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nick, I've uploaded the file.
Thanks - Anil.
On 2/14/07, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Anil,
Can you send me the orig.mgz file? You can upload it to my email address via:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Nick
On Wed, 2007-02-14 at 14:54 -0600, Anil Roy wrote:
Hi All,
I followed the steps in the tutorial on tkregister2 to align the two volumes and saved the new reg. Following this I ran recon-all again but freesurfer still quits at the watershed step. I've attached a file with the output to this email. Do you know if something else could be causing the problem.
Thanks a lot,
Anil.
On 2/12/07, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: Anil,
exclude the argument '--surf orig' from tkregister2 if the surfaces are not available. Nick On Mon, 2007-02-12 at 16:58 -0600, Anil Roy wrote: > Hi, > > I loaded up the orig volumes and the xfm. The brainmask volume isn't > there because freesurfer quit at the skull strip phase. I've attached > the tiffs of the orig and xfm to this email. As you'll see, the xfm > does look quite bad. Do you know how I could correct this. > > The manual mentions using tkregister2, but when I run it I get an > error(also attached) because the surfaces weren't generated. Is there > a different way to use tkregister2 to correct the output. > > Thanks, > > Anil > > On 2/9/07, Doug Greve < greve@nmr.mgh.harvard.edu> wrote: > Hi Anil, > > my suggestion was to first look at the volume in tkmedit > without the xfm, then, if that is oriented correctly and looks > ok, move on to the xfm > > doug > > Anil Roy wrote: > > Thanks a lot for all your input. I will check out the xfm in > > tkmedit and get back to you with the results. > > > > Anil. > > > > On 2/9/07, Doug Greve <greve@nmr.mgh.harvard.edu> wrote: > > I think the first thing you should do is visualize > > your input in tkmedit to make sure it is oriented > > correctly. FreeSurfer and AFNI may be making > > different assumptions about the data. > > > > doug > > > > > > Nick Schmansky wrote: > > > Anil, > > > > > > See this tutorial: > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > > > > > > > > > > > Also, a tool to appear in the next release, which checks the > > > talairach.xfm against a known set of proper alignments, indicates that > > > this alignment is bad. You probably will need to manually align. > > > > > > Nick > > > > > > On Thu, 2007-02-08 at 20:46 -0500, Bruce Fischl wrote: > > > > > > > you need to visualize it in tkmedit. Use file -> load transform for main > > > > volume and see if it looks reasonable (should be slightly looking down, > > > > and pretty vertical so for example the interhemispheric fissure goes > > > > > > > > > > > > straight up and down in a coronal view > > > > On Thu, 8 Feb 2007, Anil Roy wrote: > > > > > > > > > > > > > I've attached the talairach.xfm to this email. I'm a newbie to MRI analysis > > > > > so I don't know what exactly would be a red flag in this file. Please do > > > > > tell me if you see something odd. > > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > > On 2/8/07, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > > > > > > > > > > > did you check the talairach.xfm? > > > > > > On Thu, 8 Feb 2007, Anil Roy wrote: > > > > > > > > > > > > > > > > > > > Hi All, > > > > > > > > > > > > > > I installed the new build and Freesurfer still quits at the same place. > > > > > > > > > > > > > I've > > > > > > > > > > > > > attached the recon-all.log file to this email. Its still giving an error > > > > > > > > > > > > > at > > > > > > > > > > > > > the watershed step. > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > On 2/8/07, Anil Roy < aroy85@gmail.com> wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > I'll install the CentOS build and run the brain again. > > > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > > > On 2/8/07, Anil Roy > > > > > > > > > > > > > > > > < aroy85@gmail.com> wrote: > > > > > > > > > > > > > > > > > Yes. When I convert to BRIK and open with AFNI, the images show up > > > > > > > > > > > > > > > fine > > > > > > > > > > > > > > > in all three planes. > > > > > > > > > > > > > > > > > > There is some noise towards the very end but it only shows up after > > > > > > > > > > > > > > > the > > > > > > > > > > > > > > > slices with no brain tissue (or any that I can see). > > > > > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > > > > > On 2/8/07, Bruce Fischl < > > > > > > > > > > > > > > > > > > fischl@nmr.mgh.harvard.edu> wrote: > > > > > > > > > > > > > > > > > > > if you convert it to BRIK and visualize it does it look correct? > > > > > > > > > > On Thu, 8 > > > > > > > > > > Feb 2007, Anil Roy wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Hello all, > > > > > > > > > > > > > > > > > > > > > > I have some raw data and I'm not sure of the format. Its > > > > > > > > > > > > > > > > > definitely > > > > > > > > > > > > > > > > not > > > > > > > > > > > > > > > > > > > > > dicom. I ran recon-all on these files but I get an error saying > > > > > > > > > > > > > > > > > it > > > > > > > > > > > > > > > > can't > > > > > > > > > > > > > > > > > > > > > read the files. I have posted the output below. I tried to > > > > > > > > > > > > > > > > > convert > > > > > > > > > > > > > > > > the files > > > > > > > > > > > > > > > > > > > > > to afni format (BRIK + HEAD), and tried recon-all again. It ran > > > > > > > > > > > > > > > > > for > > > > > > > > > > > > > > > > a while > > > > > > > > > > > > > > > > > > > > > but gave an error that I've attached to a text file. > > > > > > > > > > > > > > > > > > > > > > Can someone please tell me how I can get Freesurfer to read these > > > > > > > > > > > > > > > > > > > > > files. I > > > > > > > > > > > > > > > > > > > > > can also upload the raw files if you'd like to take a look at > > > > > > > > > > > > > > > > > them. > > > > > > > > > > > > > > > > > Thanks a lot - Anil. > > > > > > > > > > > > > > > > > > > > > > [root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i > > > > > > > > > > > /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid > > > > > > > > > > > > > > > > > Nl-TA1-001 > > > > > > > > > > > > > > > > -sd > > > > > > > > > > > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition -all > > > > > > > > > > > INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition > > > > > > > > > > > INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with > > > > > > > > > > > > > > > > > -i, > > > > > > > > > > > > > > > > but > > > > > > > > > > > > > > > > > > > > > -force specified. > > > > > > > > > > > Deleting any previous source volumes > > > > > > > > > > > Actual FREESURFER_HOME /usr/local/freesurfer > > > > > > > > > > > -rw-rw-r-- 1 root root 76880 Feb 8 13:25 > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon- > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > all.log > > > > > > > > > > > > > > > > > Linux dhcp-129-105-146-127.speech.northwestern.edu > > > > > > > > > > > > > > > > > > > > > 2.6.17-1.2157_FC5smp #1 > > > > > > > > > > > > > > > > > > > > > SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux > > > > > > > > > > > strings: Command not found. > > > > > > > > > > > WM removal version > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 > > > > > > > > > > > > > > > > > > > > > > mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition/Nl- TA1-001/mri/orig/001.mgz > > > > > > > > > > > > > > > > > > > > > > mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition/Nl- TA1-001/mri/orig/001.mgz > > > > > > > > > > > reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > genesisRead(): can't determine file name format for > > > > > > > > > > > /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 > > > > > > > > > > > Linux > > > > > > > > > > > > > > > > > > > > > > dhcp-129-105-146-127.speech.northwestern.edu > > > > > > > > > > > > > > > > > > > > > 2.6.17-1.2157_FC5smp #1 > > > > > > > > > > > > > > > > > > > > > SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux > > > > > > > > > > > > > > > > > > > > > > recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > 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 > > > > > > > > > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu > > > > 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Anil Roy -
Bruce Fischl -
Doug Greve -
Nick Schmansky