Hello,
I am trying to work through the FS-FAST tutorial on my data. I am using OSX
10.6.8 with Freesurfer v. 5.1 When I get to the make contrast command which I
run
' mkcontrast-sess -analysis test -contrast pain-v-rest -a 1 -c 0 '
I get the following output error:
phhp-jcraggs-mb:Project
Hi
here are the commands i used to :
1) make my labels : mri_annotation2label --annotation
aparc.a2009s --hemi rh --subject ctr1 --surf pial --outdir
/home/mlaouche/makh_free/labels/ctr1
2) make the
This was the command I ran:
mri_glmfit-sim --glmdir tal.sm.wls.pct.rfx --sim mc-z 1 2
HvL.SBQ.2.1.pos --stim-sign pos
On Jun 28, 2013, at 3:29 PM, Douglas N Greve wrote:
Hi Emily, what is your mri_glmfit-sim command line?
doug
On 06/28/2013 02:40 PM, Emily Boeke wrote:
Any
Dear
Freesurfer experts,
thanks to your help I was able to install the new version and run the
„long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC
table into the cross sectional form by using “long_qdec_table” which also
worked so far. Loading that table into QDEC and
Dear
Freesurfer experts,
Or could it
be that I made a mistake creating the “Qdecrc” file?
I simply created a text file in the qdec directory and named it
“$SUBJECTS_DIR/qdec/.Qdecrc”
and put the four lines in it as advised. Should it just be named “.Qdecr” or is
there supposed to be an
doyou have matlab installed and in your path?
doug
On 07/01/2013 08:55 AM, O'Shea,Andrew wrote:
Hello,
I am trying to work through the FS-FAST tutorial on my data. I am
using OSX 10.6.8 with Freesurfer v. 5.1 When I get to the make
contrast command which I run
' mkcontrast-sess -analysis
Martin,
I'm going to experiment with data with better image quality using the
longitudinal stream. In the first step of the workflow I'm confused to what
'dcm' stands for in the following command
recon-all -all -s tpNid -i path_to_tpN_dcm
could you elaborate?
jon
On Sat, Jun 29, 2013 at
Hello all,
I currently have volumetric infant templates in .nifti format. Is there
any way to run recon-all using these templates instead of the default adult
templates? From what I understand, freesurfer uses .tif format for
templates. I just can't seem to figure out how to get the infant
Hi Peter,
it needs to be .Qdecrc and have these lines:
MEASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3 = long.thickness-pc1
MEASURE4 = long.thickness-spc
You will then see in the /Design/ tab in Qdec, that you can now select
e.g. long.thickness-rate under /Measure/ as
Hi Jon
That is one way of calling the regular recon-all stream. You point it to
any input file with the -i flag. Here dcm could be a dicom image, but
can be nifti or another format.
Best, Martin
On 07/01/2013 10:17 AM, Jonathan Holt wrote:
Martin,
I'm going to experiment with data with
Dear Freesurfer users --
I'm trying to display a SPM t map (i.e., normalized in SPM8 standard
template) in freesurfer inflated
surface for paper figure.
So, once projecting the SPM t maps into freesurfer template (e.g.,
rh.inflated), I'm wondering how I can best find out freesurfer's
Dear
Martin,
”thickness” was a typo. Can you maybe check my attached file? I suppose that I
put the four lines in it correctly. I only named it “.Qdecrc”. When I save the
file in the qdec folder of my Subject directory, the file isn´t visible anymore.
Is it supposed to be like that? It is
Hello,
Is this running in Ubuntu? If so, it should be solved by running the
following command:
$ sudo apt-get install libjpeg62
-Zeke
Dear All,
When I tried to running qdec, I'm getting the following error.
qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
shared
OK,
so I should plug the nifti's as opposed to the freesurfer generated mgzs
jon
On Jul 1, 2013, at 11:35 AM, Martin Reuter wrote:
Hi Jon
That is one way of calling the regular recon-all stream. You point it to any
input file with the -i flag. Here dcm could be a dicom image, but can be
Hi,
I have been using control points to correct excluded white matter and ran
into the same problem as Peter,
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-July/024771.html
,
in that the opposite hemisphere's boundaries recede after control points
are added and then recon-alled. Has
Log file indicates manual talairach alignment may be necessary.
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0079, pval=0. threshold=0.0050)
Manual Talairach alignment may be necessary
Can anyone provide direction. Alternatively, the error indicates
Dear Bruce,
Thank you so much for being so patient with me!
I found them
Sincerely,
Ye
On Fri, Jun 28, 2013 at 1:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Ye
there's no way a 5 minute mprage would have only 3 slices. Or any mprage
really, since they are always 3D. You
I have been trying to run tracula with a config file but keep getting the same
error message when I use the trac-all command for pre-processing
set: Variable name must begin with a letter
Attached is the text from the config file I used.
Hope to hear from you soon.
Andrew
# FreeSurfer
Resending, would greatly appreciate some input so I can move forward:
I have a fairly basic question regarding the order in which I should
perform the edits. After running the full recon on all of my subjects I
have now completed the Talairach edits and the skull strip edits on my
subjects. At
what version are you using?
On Mon, 1 Jul 2013, LIOR ZWANZIGER wrote:
Hi,I have been using control points to correct excluded white matter and ran
into the same problem
as Peter,
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-July/024771.html,
in that the opposite hemisphere's
glad to hear it
Bruce
On Mon, 1 Jul 2013, ye tian wrote:
Dear Bruce,
Thank you so much for being so patient with me!
I found them
Sincerely,
Ye
On Fri, Jun 28, 2013 at 1:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Ye
there's no way a 5 minute mprage would have
Hi Jon
have you visually inspected the results of the tal xform?
Bruce
On Mon, 1 Jul
2013, Jonathan Holt wrote:
Log file indicates manual talairach alignment may be necessary.
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0079,
pval=0.
Hi Doug,
Could you please clarify when you suggest it's best to smooth if using the
xhemi scripts? I'm a bit confused based on the emails below.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27761.html
Thank you,
Daria
From: Douglas N
Hi Daria, I would smooth the left and right separately, then compute the LI.
doug
On 07/01/2013 01:14 PM, Boratyn, Daria A. wrote:
Hi Doug,
Could you please clarify when you suggest it's best to smooth if using the
xhemi scripts? I'm a bit confused based on the emails below.
I have matlab installed. I have the following lines in my ~/matlab/startup.m
file
% FreeSurfer FAST %
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
if (exist(fsfasttoolbox) == 7)
path(path,fsfasttoolbox);
end
I have been trying to run tracula with a config file but keep getting the same
error message when I use the trac-all command for pre-processing
set: Variable name must begin with a letter
Its become very annoying.
___
Freesurfer mailing list
I have been trying to run tracula with a config file but keep getting the same
error message when I use the trac-all command for pre-processing
set: Variable name must begin with a letter
It has become very, very annoying. PLEASE SOMEONE HELP!!!
Andrew
--
# FreeSurfer SUBJECTS_DIR
#
Hi Peter,
file looks good, you could try adding a newline at the end. The file
should be hidden (all files starting with a . are hidden). Not sure why
you cannot select the rate as the measure. Is your environment variable
($SUBJECTS_DIR) setup correctly?
Best, Martin
On 07/01/2013 12:00
Hi Jon,
this is for the cross sectional stream, so it is the same as what you
did when you processed your data independently. You point recon all to
some input file and it generates the subject/mri/orig/001.mgz etc . You
can also do this in two steps, the -i to import your data and then the
Open a terminal and run matlab
On 07/01/2013 01:29 PM, O'Shea,Andrew wrote:
I have matlab installed. I have the following lines in my
~/matlab/startup.m file
% FreeSurfer FAST %
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox =
I have tried to inspect the tal xfms that were created in the brief time
this string was running
recon-all -all -s tpNid -i path_to_tpN_dcm
while viewing orig.mgz in tkmedit. they were talairach.xfm and
talairach.auto.xfm, both were empty and the tkmedit window was empty.
upon further
Hi Folks,
Once we make control points in tkmedit, they are stored in the file
control.dat
Are these control points stored in RAS co-ordinate system ?
If not what is the co-ordinate system used to store the control points
Thanks
Mehul
___
Freesurfer
Martin,
I did find that info and tried to follow the instructions, but you'll see
based on my last message the talairach files didn't seem to contain
anything?
On Mon, Jul 1, 2013 at 2:29 PM, Jonathan Holt whats...@umich.edu wrote:
I have tried to inspect the tal xfms that were created in
yes, they are stored in ras
On Mon, 1 Jul 2013, Mehul Sampat wrote:
Hi Folks, Once we make control points in tkmedit, they are stored in the
file control.dat
Are these control points stored in RAS co-ordinate system ?
If not what is the co-ordinate system used to store the control points
Thanks
Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a
deep breath and let it all go.
More to the point, when I view the text file that you sent, I see that
several of the lines are joined together, so both the dcmroot and dcmlist
variables appear commented out. Is this
Hi Jon,
are you passing your images?
tpNid is a placeholder for the id of your subject+time point, for
example it could be jon_01 the path_to_tpN_dcm needs to specify the
path to the dicom files, point it to the first file in the MPRAGE series
(or multi echo mprage or what you are using).
Hi Jon,
this is not really a longitudinal problem. You can look at this tutorial
on how to check/fix bad talairach:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview
Best, Martin
On 07/01/2013 01:03 PM, Bruce Fischl wrote:
Hi Jon
have you visually inspected the
Hi Doug,
I am using w files to show ECoG activation at localized regions on the
cortex. So preferably, I would like to show temporal dynamics too (thus the
multi-frame question, and thanks for pointing me to MNE).
What will replace w files going forward? i think w file's file format is
very
Hi,
I want to obtain volume statistics from a ROI in fsaverage.
I have register.dat and a .nii file (the ROI), but I don't now how to get
to the .label.
The last try has been:
mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/label/ROI.nii
--o $SUBJECTS_DIR/fsaverage/label/ROI.mgh
--reg
Can you see that this is all one line?
# Input diffusion DICOMs (file names relative to dcmroot) # If original
DICOMs don't exist, these can be in other image format # but then bvecfile
and bvalfile must be specified (see below) # set dcmroot =
/home/baileype/Desktop/JG005 set dcmlist =
I am new to FreeSurfer and have been tasked with running a large number of
subjects through the pipeline. I wanted to inquire about the benefits of
manually editing the output data at each step as outlined by the manual. Is
there anything in the literature regarding the differences, if any,
Thanks Bruce;
I noticed that in the control.dat file the second last line is useRealRAS
0
just curious to know if info is used by recon-all or is only used by the
viewer ?
Thanks
Mehul
On Mon, Jul 1, 2013 at 11:34 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
yes, they are stored in ras
What program are you viewing it in? If you add a line at the end of
config.txt that says echo $dcmlist (without the quotation marks) and
then run source config.txt on the command line, does it print out
DKI.nii.gz?
On Mon, 1 Jul 2013, Gundran, Andrew wrote:
It reads like
# Input
Martin,
definitely passing my images and naming time points appropriately. I have been
passing nifti as opposed to dicom and it's entirely possible that may be the
issue?
jon
On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:
Hi Jon,
are you passing your images?
tpNid is a placeholder for
Hi Mehul
they can either be in real (meaning scanner) RAS or in surface RAS
cheers
Bruce
On Mon,
1 Jul 2013, Mehul Sampat wrote:
Thanks Bruce; I noticed that in the control.dat file the second last line is
useRealRAS 0
just curious to know if info is used by recon-all or is only used by the
Dear Liane,
I am in the same position as you. I really hope that someone can give a
hint, too.
Sincerely,
Ye
On Mon, Jul 1, 2013 at 1:57 PM, Liane Hunter
liane.hun...@med.einstein.yu.edu wrote:
I am new to FreeSurfer and have been tasked with running a large number
of subjects through
it really depends on data quality. We typically only do manual
interventions for large-scale errors or if they are in regions that we
want to investigate strong prior hypotheses about
cheers
Bruce
On Mon, 1 Jul 2013, ye
tian wrote:
Dear Liane,
I am in the same position as you. I really
We have already started putting this data into mgh/mgz file (and even
nifti).
doug
On 07/01/2013 02:39 PM, Zhongtian Dai wrote:
Hi Doug,
I am using w files to show ECoG activation at localized regions on the
cortex. So preferably, I would like to show temporal dynamics too
(thus the
No, it's not nifti, that should work.
Can you send me your log file and the command you issued.
Thanks, Martin
On 07/01/2013 03:13 PM, Jonathan Holt wrote:
Martin,
definitely passing my images and naming time points appropriately. I
have been passing nifti as opposed to dicom and it's
That probably means you're not running a C shell. That's fine, can you
instead try running trac-all and see if it prints out the value of
dcmlist now that you've added that line?
I'll repeat my other question: What program are you using to view the text
file?
On Mon, 1 Jul 2013, Gundran,
Thanks Bruce;
Okay i assume, useRealRAS should be 1 for scanner RAS;
Two questions:
1. If my control points are in scanner RAS, then can I use them directly as
long as I set
useRealRAS to 1 in the control.dat file ?
2. Can useRealRAS variable be only 0/1 or do you have a different value for
I thought mgh (or nifti) is meant to store volume data. How do one
associate vertex weights to a surface from mgh? Maybe I can find some
documentation for writing/reading such data into mgh somewhere?
On Mon, Jul 1, 2013 at 2:33 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
We have
1. Yes, I think so, although I wouldn't swear that everything is smart
enough to read this flag. You might be safer converting them to surface ras
and using them that way
2. Yes.
On Mon, 1 Jul 2013, Mehul Sampat wrote:
Thanks Bruce; Okay i assume, useRealRAS should be 1 for scanner RAS;
Hi
can you send part of recon-all.log and do recon-all -i 242.nii.gz -s
242_FS -nuintensitycor-3T -nocanorm -openmp 8 -use-cuda -hippo-subfields
-all -debug
Knut J
On 06/29/2013 06:06 PM, Salil Soman wrote:
Hi,
I am running freesurfer 5.3 on an ubuntu 13.04 with a nvidia card and
the
Thanks Bruce.
Okay will convert them from scanner RAS to surface RAS;
last question: I looked at the control points made from tkmedit;
it seems like you round of the co-ordinates to integers and then save them
as floats;
Does the co-ordinate information saved in control.dat need to be rounded
or
Hi Mehul
writing as full floats should be fine, I didn't realize tkmedit rounded
Bruce
On Mon, 1 Jul 2013, Mehul Sampat wrote:
Thanks Bruce.
Okay will convert them from scanner RAS to surface RAS; last question: I
looked at the control points made from tkmedit;
it seems like you round of the
Hi again,
is it possible to use mri_convert with a register.dat to create a .mgh
volume in the registered space?
any help would be appreciated...
thanks!
Gari
On Mon, Jul 1, 2013 at 8:45 PM, Garikoitz Lerma-Usabiaga
gariko...@gmail.com wrote:
Hi,
I want to obtain volume statistics from a
Hi Gari
you can certainly do this with mri_vol2vol. You can try mri_convert, I
think it reads .dat files, but vol2vol definitely does
cheers
Bruce
On Mon, 1 Jul 2013,
Garikoitz Lerma-Usabiaga wrote:
Hi again,
is it possible to use mri_convert with a register.dat to create a .mgh
volume in
Dear freesurfers,
After running recon-all -s Subject -autorecon1, I checked the status.log
file, it seems to have two contradictory statements:
#@# *Talairach Failure Detection* Mon Jul 1 13:00:30 CDT 2013
recon-all -s Barba50527_2 finished *without error* at Mon Jul 1 13:23:15
CDT 2013
When
Hi Ye
I think that means that the failure detection was run, not that it found
anything wrong.
cheers
Bruce
On Mon, 1 Jul 2013, ye tian wrote:
Dear freesurfers,
After running recon-all -s Subject -autorecon1, I checked the status.log
file, it seems to have two contradictory statements:
#@#
Dear Bruce,
Thank you very much! What a relief!
Sincerely,
Ye
On Mon, Jul 1, 2013 at 5:25 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Ye
I think that means that the failure detection was run, not that it found
anything wrong.
cheers
Bruce
On Mon, 1 Jul 2013, ye tian wrote:
use mri_vol2vol
doug
On 7/1/13 5:07 PM, Garikoitz Lerma-Usabiaga wrote:
Hi again,
is it possible to use mri_convert with a register.dat to create a .mgh
volume in the registered space?
any help would be appreciated...
thanks!
Gari
On Mon, Jul 1, 2013 at 8:45 PM, Garikoitz Lerma-Usabiaga
hi anastasia,
i'm trying to debug a seg fault that some folks are seeing deep into a
tracula run.
process:
1. feed dicoms to a script that runs DTIPrep and outputs a nifti file,
bvec, bval
(among checking for many artifacts, this reduces the b=0 volumes to a
single registered mean volume, runs
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