[Freesurfer] Need some materials
Dear Freesurfer Experts, I am a senior, and I am going to finish my graduation thesis which is about the use of freesurfer.So I need some written materials,such as the development history of Freesurfer, the achievement of Freesurfer and so on. But I don't know. Can you help me? Or give me some wed pages. Thanks in advance. Yours Bobo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] 1-way ANOVA: contrast specification
Dear Freesurfers, I'm going to run 1-way anova, followed by post hoc pairwise comparison. My factor-of-interest has 4 levels and, in addition, I would like to regress out the effects of 3 continious variables. I have attached my *fsgd-file. Therefore, my first *mtx-file should contain the following: 0.5 -0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 Correct? Thank you very much beforehand! === Regards, Alexander Lebedev Stavanger University Hospital All_Dep.fsgd Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all exiting with errors
Dear FreeSurfer experts, I am trying to recon-all T1 images with the command recon-all -s subjectname -i /path/to/subject/directory/subject.nii.gz. This command used to work with several images, but one of my images is always exiting with errrors, in my opinion without a reason. Any suggestions what is going on? I am attaching the recon-all.log of my data. Thanks for your help, Julia Mon May 14 20:00:03 CEST 2012 /dat/Bildgebung/BPD/Cortical_thickness/1026 /usr/local/freesurfer/bin/recon-all -s 1026 -i /dat/Bildgebung/BPD/Cortical_thickness/1026.nii.gz subjid 1026 setenv SUBJECTS_DIR /dat/Bildgebung/BPD/Cortical_thickness FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux wkjp05 3.0.0-19-generic #33-Ubuntu SMP Thu Apr 19 19:05:14 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 13845 maxlocks unlimited maxsignal13845 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 17960401743936 52104 0340 22092 -/+ buffers/cache:1721504 74536 Swap: 18329561655632 177324 program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ### /dat/Bildgebung/BPD/Cortical_thickness/1026 mri_convert /dat/Bildgebung/BPD/Cortical_thickness/1026.nii.gz /dat/Bildgebung/BPD/Cortical_thickness/1026/mri/orig/001.mgz Linux wkjp05 3.0.0-19-generic #33-Ubuntu SMP Thu Apr 19 19:05:14 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1026 exited with ERRORS at Mon May 14 20:00:35 CEST 2012 To report a problem, see 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future
you need to call mris_make_surfaces directly. It's a bit complicated as you need to intensity normalize and register the hires volume to the surfaces first. I have an example script if anyone is interested, but no one has used it yet but me I don't think (unless Matt Glasser has gotten his version working, which on second thought he probably has) On Mon, 14 May 2012, Michael Waskom wrote: Hi Bruce, Is there a flag for this on recon-all? Or do you need to use mri_make_surfaces directly? Best, Michael On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Joshua yes, we already have upgraded mris_make_surfaces to take higher res data and refine the surfaces with it. Haven't tried it on the aseg yet, but if you upload a sample dataset I could see how hard it is. cheers Bruce On Mon, 14 May 2012, Joshua Lee wrote: Dear Freesurfers, Over the last years, MR imaging technology hasimproved such that sub 1-mm isotropic scans can be obtained with good signal to noise characteristics. For example, our lab uses 0.7mm isotropic structural MR images. I understand that the Freesurfer pipeline will up-sample these to 1mm isotropic, but it seems a shame that so much information is left unused which could be used to improve the accuracy of sub-cortical and cortical segmentation. My question is whether there are any plans at Freesurfer to change the reference standard resolution from 1mm isotropic, or provide another solution that can help researchers make the most of your technology. Sincerely, Joshua - Joshua ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Need some materials
Hi Bobo try this: http://www.ncbi.nlm.nih.gov/pubmed/22248573 cheers Bruce On Tue, 15 May 2012, bowan...@mail.ustc.edu.cn wrote: Dear Freesurfer Experts, I am a senior, and I am going to finish my graduation thesis which is about the use of freesurfer.So I need some written materials,such as the development history of Freesurfer, the achievement of Freesurfer and so on. But I don't know. Can you help me? Or give me some wed pages. Thanks in advance. Yours Bobo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all exiting with errors
Hi Julia I don't see any error messages. If you upload the dataset we'll take a look. Make sure you have enough ram in the machine (2G) and free disk space. cheers Bruce On Tue, 15 May 2012, Richter, Julia wrote: Dear FreeSurfer experts, I am trying to recon-all T1 images with the command recon-all -s subjectname -i /path/to/subject/directory/subject.nii.gz. This command used to work with several images, but one of my images is always exiting with errrors, in my opinion without a reason. Any suggestions what is going on? I am attaching the recon-all.log of my data. Thanks for your help, Julia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future
Yes, I have a modified script working. For the white surface, the essentials are the same as Bruce's script but it has some additional stuff (e.g register T2w to T1w), and I call it in the middle of the recon-all rather than at the end. For the pial surface, I have done some more complicated stuff, which I'd love to talk to Bruce about some more some time. :) Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, May 15, 2012 7:29 AM To: Michael Waskom Cc: FreeSurfer Subject: Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future you need to call mris_make_surfaces directly. It's a bit complicated as you need to intensity normalize and register the hires volume to the surfaces first. I have an example script if anyone is interested, but no one has used it yet but me I don't think (unless Matt Glasser has gotten his version working, which on second thought he probably has) On Mon, 14 May 2012, Michael Waskom wrote: Hi Bruce, Is there a flag for this on recon-all? Or do you need to use mri_make_surfaces directly? Best, Michael On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Joshua yes, we already have upgraded mris_make_surfaces to take higher res data and refine the surfaces with it. Haven't tried it on the aseg yet, but if you upload a sample dataset I could see how hard it is. cheers Bruce On Mon, 14 May 2012, Joshua Lee wrote: Dear Freesurfers, Over the last years, MR imaging technology hasimproved such that sub 1-mm isotropic scans can be obtained with good signal to noise characteristics. For example, our lab uses 0.7mm isotropic structural MR images. I understand that the Freesurfer pipeline will up-sample these to 1mm isotropic, but it seems a shame that so much information is left unused which could be used to improve the accuracy of sub-cortical and cortical segmentation. My question is whether there are any plans at Freesurfer to change the reference standard resolution from 1mm isotropic, or provide another solution that can help researchers make the most of your technology. Sincerely, Joshua - Joshua ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem creating longitudinal template file
Hi Martin,
I think this is what you're looking for. If not, let me know.
recon-all -base 137_S_0158_template -tp
/Applications/freesurfer/subjects/corinna/ADNI/BL/137_S_0158/mri/norm.mgz
-tp
/Applications/freesurfer/subjects/corinna/ADNI/12mos/137_S_0158/mri/norm.mgz
-tp
/Applications/freesurfer/subjects/corinna/ADNI/24mos/137_S_0158/mri/norm.mgz
-tp
/Applications/freesurfer/subjects/corinna/ADNI/36mos/137_S_0158/mri/norm.mgz
-all
So it will create this for each of the subjects.
There are folders for each time point and then the subjects within those
folders.
Corinna
On Mon, May 14, 2012 at 10:29 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu
wrote:
Hi corinna,
Can you send the corresponding call to recon-all that your script
generates?
Best Martin
On May 14, 2012, at 18:27, Corinna Bauer corinna...@gmail.com wrote:
Hello all,
I am trying to create a template for longitudinal processing and am
running into some problems generating the file. I have many subjects so I
am running a batch script. I am using version 5.1.0
Any suggestions?
Thanks!
Corinna
Here is my script:
#!/bin/tcsh
setenv FREESURFER_HOME /Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/corinna/ADNI/template
set subjects=`cat $1`
foreach subject ($subjects)
echo Processing $subject
-
set subj_dir=/Applications/freesurfer/subjects/corinna/ADNI/
set
template=/Applications/freesurfer/subjects/corinna/ADNI/template/${subject}_template/mri
set
tp_BLmos=/Applications/freesurfer/subjects/corinna/ADNI/BL/${subject}/mri/norm.mgz
set
tp_12mos=/Applications/freesurfer/subjects/corinna/ADNI/12mos/${subject}/mri/norm.mgz
set
tp_24mos=/Applications/freesurfer/subjects/corinna/ADNI/24mos/${subject}/mri/norm.mgz
set
tp_36mos=/Applications/freesurfer/subjects/corinna/ADNI/36mos/${subject}/mri/norm.mgz
#set nu_mgz=${subj_dir}/mri/nu.mgz
recon-all -base ${subject}_template -tp ${tp_BLmos} -tp ${tp_12mos}
-tp ${tp_24mos} -tp ${tp_36mos} -all
end
Here is my output:
Processing 137_S_0631 -
Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is
/Applications/freesurfer/subjects/corinna/ADNI/template
Actual FREESURFER_HOME /Applications/freesurfer
Darwin http://ebrcb-dhcp-240-126.bumc.bu.edu
ebrcb-dhcp-240-126.bumc.bu.edu 10.4.2 Darwin Kernel Version 10.4.2: Tue
Jul 27 21:17:17 PDT 2010; root:xnu-1504.7.60~1/RELEASE_X86_64 x86_64
#
#@# Longitudinal Base Subject Creation Mon May 14 18:21:23 EDT 2012
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template
\n mri_robust_template --mov
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
--lta
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta
--template
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz
--average 1 --sat 4.685 \n
$Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $
--mov: Using
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
as movable/source volume.
--mov: Using
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
as movable/source volume.
--mov: Using
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
as movable/source volume.
--mov: Using
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
as movable/source volume.
Total: 4 input volumes
--lta: Will output LTA transforms
--template: Using
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz
as template output volume.
--average: Using method 1 for template computation.
--sat: Using saturation 4.685 in M-estimator!
reading source
'/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz'...
mghRead(/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz,
-1): could not open file
MultiRegistration::loadMovables: could not open
[Freesurfer] confusion with tkregister2
Morning all, I ran the recon yesterday, and it says it ran without error. I am now running tkregister2, but for some reason when i compare the coronal view, things look okay on the mri, but it looks like the axial view for the CT. I'm not sure in which step this happened? Thanks, Mia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] lGI differences without variation in other cortical morphometric variables
Dear all, I am comparing a group of patients with controls. I extracted: cortical volume, surface area, cortical thickness and gyrification index for each subject's lobe. Comparisons between this variables with Total Intracranial Volume as a covariate indicated a difference in frontal and temporal lobes lGI. However, differences were not significant for any of the other variables. I can´t understand these results from a biological perspective. I was expecting that if a difference exist in lGI it would also manifest in surface area or volume. Can someone help me with an explanation for this? Thank you. ines ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Problem creating longitudinal template file
Hi Corinna,
you need a single folder with all subjects and all time point:
so the subjects directory will look like:
me1
me2
me3
you1
you2
...
You can create such a folder and insert symbolic links to the original
subject folders if you want to keep your structure.
Then create the base in this folder for each subject and then the
longitudinals. You either need to path this folder via the environment
variable SUBJECTS_DIR, or on the command line to recon-all via the -sd
switch.
Also, the -tp stpid needs only the subject time point id. So in my
example above this would be:
recon-all -base me -tp me1 -tp me2 -tp me3 -all
it will create the directory 'me'. Don't pass full pathnames or even a
file name (you passed the norm.mgz).
Best, Martin
On Tue, 2012-05-15 at 09:54 -0400, Corinna Bauer wrote:
Hi Martin,
I think this is what you're looking for. If not, let me know.
recon-all -base 137_S_0158_template
-tp /Applications/freesurfer/subjects/corinna/ADNI/BL/137_S_0158/mri/norm.mgz
-tp
/Applications/freesurfer/subjects/corinna/ADNI/12mos/137_S_0158/mri/norm.mgz
-tp
/Applications/freesurfer/subjects/corinna/ADNI/24mos/137_S_0158/mri/norm.mgz
-tp
/Applications/freesurfer/subjects/corinna/ADNI/36mos/137_S_0158/mri/norm.mgz
-all
So it will create this for each of the subjects.
There are folders for each time point and then the subjects within
those folders.
Corinna
On Mon, May 14, 2012 at 10:29 PM, Martin Reuter
mreu...@nmr.mgh.harvard.edu wrote:
Hi corinna,
Can you send the corresponding call to recon-all that your
script generates?
Best Martin
On May 14, 2012, at 18:27, Corinna Bauer
corinna...@gmail.com wrote:
Hello all,
I am trying to create a template for longitudinal processing
and am running into some problems generating the file. I
have many subjects so I am running a batch script. I am
using version 5.1.0
Any suggestions?
Thanks!
Corinna
Here is my script:
#!/bin/tcsh
setenv FREESURFER_HOME /Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
setenv
SUBJECTS_DIR /Applications/freesurfer/subjects/corinna/ADNI/template
set subjects=`cat $1`
foreach subject ($subjects)
echo Processing $subject
-
set
subj_dir=/Applications/freesurfer/subjects/corinna/ADNI/
set
template=/Applications/freesurfer/subjects/corinna/ADNI/template/${subject}_template/mri
set
tp_BLmos=/Applications/freesurfer/subjects/corinna/ADNI/BL/${subject}/mri/norm.mgz
set
tp_12mos=/Applications/freesurfer/subjects/corinna/ADNI/12mos/${subject}/mri/norm.mgz
set
tp_24mos=/Applications/freesurfer/subjects/corinna/ADNI/24mos/${subject}/mri/norm.mgz
set
tp_36mos=/Applications/freesurfer/subjects/corinna/ADNI/36mos/${subject}/mri/norm.mgz
#set nu_mgz=${subj_dir}/mri/nu.mgz
recon-all -base ${subject}_template -tp ${tp_BLmos} -tp
${tp_12mos} -tp ${tp_24mos} -tp ${tp_36mos} -all
end
Here is my output:
Processing 137_S_0631
-
Subject Stamp:
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Current Stamp:
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
INFO: SUBJECTS_DIR
is /Applications/freesurfer/subjects/corinna/ADNI/template
Actual FREESURFER_HOME /Applications/freesurfer
Darwin ebrcb-dhcp-240-126.bumc.bu.edu 10.4.2 Darwin Kernel
Version 10.4.2: Tue Jul 27 21:17:17 PDT 2010;
root:xnu-1504.7.60~1/RELEASE_X86_64 x86_64
#
#@# Longitudinal Base Subject Creation Mon May 14 18:21:23
EDT 2012
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template
\n mri_robust_template
--mov
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
--lta
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta
[Freesurfer] low eff and VRF values
(1) Version: optseq2.c,v 2.21.2.1 (2) Computer operating system: Mac OS X Version 10.7.3 (3) Command line: optseq2 --ntp 230 --tr 1.5 --psdwin 0 24 0.5 --ev go 7 36 --ev nogo 7 12 --nkeep 4 --o gonogo --nsearch 1000 (4) Description of the problem: This is in reference to a go/no-go paradigm. I am getting very low Eff and VRFAvg values. Is this an issue/ is common with go/no-go paradigms? If this is an issue, any recommendations for appropriate modifications. A trial in my experiment involves a countdown (duration 2 seconds) followed by the event of interest (0.5 seconds) followed by a blank screen (3.5 seconds). I set dPSD at 0.5 because this number is divisible by both the --tr and trial length (7 seconds). (5) Log and/or summary files: Searched 1000 iterations for 0.002500 hours Rate: 111.111 iterations per second INFO: 211/1000 schedules were ill-conditioned Number of iterations since last substitution 310 Cost Avg/Std: 0.0105840 0.0060667 Max Eff Encountered:0.0154867 Max VRFAvg Encountered: 1.6717 Eff of Nominal Ideal XtX: 0.177183 Rank Cost ZCost NthIter Eff CB1Err VRFAvg VRFStd VRFMin VRFMax VRFRng IXtXErr 10.0155 0.808 597 0.015 0.157407 1.67 0.61 0.80 4.13 3.33 4723.04 20.0150 0.732 218 0.015 0.009259 1.58 0.50 0.87 3.03 2.15 4749.02 30.0149 0.70882 0.015 0.009259 1.54 0.46 0.91 3.15 2.24 4882.85 40.0148 0.703 539 0.015 0.175926 1.56 0.52 0.94 3.86 2.91 4752.15 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] lGI differences without variation in other cortical morphometric variables
Hi, Thank you so much for your reply. I am going to read the paper. However, if the increase in head size obscures the lGI, why this is not an overall variation? Meaning, why is only for the frontal and temporal lobes? thank you ines On Tue, May 15, 2012 at 4:30 PM, j janssen joost.jansse...@gmail.com wrote: Hi, I am comparing a group of patients with controls. I extracted: cortical volume, surface area, cortical thickness and gyrification index for each subject's lobe. Comparisons between this variables with Total Intracranial Volume as a covariate indicated a difference in frontal and temporal lobes lGI. what happens if you do not adjust for intracranial volume? if your patients have abnormal sized lobes then this may be obscured by controlling for head size. However, differences were not significant for any of the other variables. I can´t understand these results from a biological perspective. I was expecting that if a difference exist in lGI it would also manifest in surface area or volume. this paper: http://www.ncbi.nlm.nih.gov/pubmed/18267953 tells us that it is possible for smaller sized brains to have higher folding compared to bigger sized brains. however, it also states that it's much more probable for bigger sized brains to have a higher degree of folding, indeed a strong relationship is shown between brain volume, cortical surface and folding (Figs. 3 and 4c) over large parts of the cortex. hth, -joost Can someone help me with an explanation for this? Thank you. ines ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] low eff and VRF values
You're getting very low VRFs because of the sub-TR estimation (TR=1.5, but TER=0.5), so you reduce your power to about 1/3. This is not a problem unless you analyze your data using an FIR. If you assume a shape, then the power will come back. doug On 05/15/2012 11:41 AM, Andrew Valdespino wrote: (1) Version: optseq2.c,v 2.21.2.1 (2) Computer operating system: Mac OS X Version 10.7.3 (3) Command line: optseq2 --ntp 230 --tr 1.5 --psdwin 0 24 0.5 --ev go 7 36 --ev nogo 7 12 --nkeep 4 --o gonogo --nsearch 1000 (4) Description of the problem: This is in reference to a go/no-go paradigm. I am getting very low Eff and VRFAvg values. Is this an issue/ is common with go/no-go paradigms? If this is an issue, any recommendations for appropriate modifications. A trial in my experiment involves a countdown (duration 2 seconds) followed by the event of interest (0.5 seconds) followed by a blank screen (3.5 seconds). I set dPSD at 0.5 because this number is divisible by both the --tr and trial length (7 seconds). (5) Log and/or summary files: Searched 1000 iterations for 0.002500 hours Rate: 111.111 iterations per second INFO: 211/1000 schedules were ill-conditioned Number of iterations since last substitution 310 Cost Avg/Std: 0.0105840 0.0060667 Max Eff Encountered:0.0154867 Max VRFAvg Encountered: 1.6717 Eff of Nominal Ideal XtX: 0.177183 Rank Cost ZCost NthIter Eff CB1Err VRFAvg VRFStd VRFMin VRFMax VRFRng IXtXErr 10.0155 0.808 597 0.015 0.157407 1.67 0.61 0.80 4.13 3.33 4723.04 20.0150 0.732 218 0.015 0.009259 1.58 0.50 0.87 3.03 2.15 4749.02 30.0149 0.70882 0.015 0.009259 1.54 0.46 0.91 3.15 2.24 4882.85 40.0148 0.703 539 0.015 0.175926 1.56 0.52 0.94 3.86 2.91 4752.15 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] A doubt with the group analysis of longitudinal data
That will be fine. We are working on tools to perform mixed effects analysis on longitudinal, but they are not ready yet. I think Martin has some tools to exploit the fact that they are longitudinal (eg, computing a slope normalizing by the first time point or the average of the time points). But what you have is also fine too. doug On 05/14/2012 11:10 PM, jorge luis wrote: Hi all I have some longitudinal data ready for the group analysis but I have a doubt: Can I simply use the following command to resample all left hemisphere thickness maps onto the fsaverage surface (as in traditional cross-sectional analyses)? mris_preproc --fsgd fsgd.txt --target fsaverage --hemi lh --meas thickness --out lh.fsgd_subj.mgh Is there any change because of the data being longitudinal? Thanks -Jorge ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] 1-way ANOVA: contrast specification
Hi Alexander, what you have there looks like an interaction test for a 2x2 ANOVA. If you are looking for an effect of level, then you will need something like 1 -1 0 0 1 0 -1 0 1 0 0 -1 Plus 12 zeros on each line for the covariates. I would also first test for an interaction in the covariates. If there is no interaction, then re-run with a DOSS model. doug On 05/15/2012 05:17 AM, Александр Лебедев wrote: Dear Freesurfers, I'm going to run 1-way anova, followed by post hoc pairwise comparison. My factor-of-interest has 4 levels and, in addition, I would like to regress out the effects of 3 continious variables. I have attached my *fsgd-file. Therefore, my first *mtx-file should contain the following: 0.5 -0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 Correct? Thank you very much beforehand! === Regards, Alexander Lebedev Stavanger University Hospital= ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] confusion with tkregister2
Hi Mia, you'll have to give us more information, eg, what was your command line for tkregister2? On 05/15/2012 09:56 AM, Borzello, Mia wrote: Morning all, I ran the recon yesterday, and it says it ran without error. I am now running tkregister2, but for some reason when i compare the coronal view, things look okay on the mri, but it looks like the axial view for the CT. I'm not sure in which step this happened? Thanks, Mia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Clusters size treshold question
Dear All, I would like to know if there is a way to eliminate from my significant clusters (grf.th3.pos.sig.cluster.mgh) obtained after running mri_glmfit-sim with grf option and using mri_volcluster the clusters with a size smaller than 50 mm^3 or in other words to keep only clusters with a volume/size greater than 50 mm^3. Thank you for your time and help. Regards, Antonella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Clusters size treshold question
Keep changing the --cwpvalthresh until all clusters smaller than 50 are gone. doug On 05/15/2012 12:43 PM, Antonella Kis wrote: Dear All, I would like to know if there is a way to eliminate from my significant clusters (grf.th3.pos.sig.cluster.mgh) obtained after running mri_glmfit-sim with grf option and using mri_volcluster the clusters with a size smaller than 50 mm^3 or in other words to keep only clusters with a volume/size greater than 50 mm^3. Thank you for your time and help. Regards, Antonella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Inter-hemispheric registration issue
Dear all, I'm trying to use the new script for the inter-hemisphere analysis, in Fs version 5.0. I have downloaded the files as suggested (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html). Surfreg seems to be running fine (surfreg --s subject --t fsaverage_sym --lh), but I have problems then with the --xhemi option. Some files appear to be missing, I get the following error messages: ERROR: cannot find /path/subject/xhemi/surf/lh.sphere ERROR: cannot find /path/subject/xhemi/surf/lh.smoothwm ERROR: cannot find /path/subject/xhemi/surf/lh.sphere ERROR: cannot find /path/subject/xhemi/label/lh.aparc.annot lh.fsaverage_sym.sphere.reg is created in $subject as it should (please find the surfreg log below). Thank you in advance, Irene Log file for surfreg samedi 12 mai 2012, 17:36:31 (UTC+0200) setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ cd /home/ialtarelli /home/ialtarelli/freesurfer/bin/surfreg --s aa_copie --t fsaverage_sym --lh Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 x86_64 GNU/Linux #@# lh samedi 12 mai 2012, 17:36:31 (UTC+0200) #CMD# mris_register -curv -annot aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg using smoothwm curvature for final alignment zeroing medial wall in aparc.annot $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading surface from /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading template parameterization from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... ripping medial wall... writing registered surface to /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.007, std = 0.603 curvature mean = 0.030, std = 0.806 curvature mean = 0.024, std = 0.853 curvature mean = 0.009, std = 0.826 curvature mean = 0.011, std = 0.936 curvature mean = 0.003, std = 0.836 curvature mean = 0.005, std = 0.972 curvature mean = 0.001, std = 0.837 curvature mean = 0.001, std = 0.988 curvature mean = -0.032, std = 0.312 curvature mean = 0.032, std = 0.124 curvature mean = 0.079, std = 0.315 curvature mean = 0.031, std = 0.151 curvature mean = 0.049, std = 0.489 curvature mean = 0.031, std = 0.165 curvature mean = 0.028, std = 0.631 curvature mean = 0.031, std = 0.171 curvature mean = 0.011, std = 0.749 159: 0 negative triangles surfreg-Run-Time-Hours aa_copie lh 0 0,84 samedi 12 mai 2012, 18:26:49 (UTC+0200) surfreg done -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Inter-hemispheric registration issue
Hi Irene, can you send the log file for the command that is failing? doug On 05/15/2012 01:28 PM, Irene Altarelli wrote: Dear all, I'm trying to use the new script for the inter-hemisphere analysis, in Fs version 5.0. I have downloaded the files as suggested (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html). Surfreg seems to be running fine (surfreg --s subject --t fsaverage_sym --lh), but I have problems then with the --xhemi option. Some files appear to be missing, I get the following error messages: ERROR: cannot find /path/subject/xhemi/surf/lh.sphere ERROR: cannot find /path/subject/xhemi/surf/lh.smoothwm ERROR: cannot find /path/subject/xhemi/surf/lh.sphere ERROR: cannot find /path/subject/xhemi/label/lh.aparc.annot lh.fsaverage_sym.sphere.reg is created in $subject as it should (please find the surfreg log below). Thank you in advance, Irene Log file for surfreg samedi 12 mai 2012, 17:36:31 (UTC+0200) setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ cd /home/ialtarelli /home/ialtarelli/freesurfer/bin/surfreg --s aa_copie --t fsaverage_sym --lh Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 x86_64 GNU/Linux #@# lh samedi 12 mai 2012, 17:36:31 (UTC+0200) #CMD# mris_register -curv -annot aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg using smoothwm curvature for final alignment zeroing medial wall in aparc.annot $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading surface from /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading template parameterization from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... ripping medial wall... writing registered surface to /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.007, std = 0.603 curvature mean = 0.030, std = 0.806 curvature mean = 0.024, std = 0.853 curvature mean = 0.009, std = 0.826 curvature mean = 0.011, std = 0.936 curvature mean = 0.003, std = 0.836 curvature mean = 0.005, std = 0.972 curvature mean = 0.001, std = 0.837 curvature mean = 0.001, std = 0.988 curvature mean = -0.032, std = 0.312 curvature mean = 0.032, std = 0.124 curvature mean = 0.079, std = 0.315 curvature mean = 0.031, std = 0.151 curvature mean = 0.049, std = 0.489 curvature mean = 0.031, std = 0.165 curvature mean = 0.028, std = 0.631 curvature mean = 0.031, std = 0.171 curvature mean = 0.011, std = 0.749 159: 0 negative triangles surfreg-Run-Time-Hours aa_copie lh 0 0,84 samedi 12 mai 2012, 18:26:49 (UTC+0200) surfreg done -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future
Hi Bruce and Michael, That would be very nice. Do I just email you the hi-res *whole-brain*mprages, or is their another way to get the images to you? On the other hand, I'm a fair hand at scripting. I'd be willing to experiment with any scripts that you might provide. Last, and on an unrelated note. Is that programming position at Freesurfer still open? I know someone looking for an interesting and challenging position like that. Best, Joshua - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 On Tue, May 15, 2012 at 6:00 AM, Matt Glasser m...@ma-tea.com wrote: Yes, I have a modified script working. For the white surface, the essentials are the same as Bruce's script but it has some additional stuff (e.g register T2w to T1w), and I call it in the middle of the recon-all rather than at the end. For the pial surface, I have done some more complicated stuff, which I'd love to talk to Bruce about some more some time. :) Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, May 15, 2012 7:29 AM To: Michael Waskom Cc: FreeSurfer Subject: Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future you need to call mris_make_surfaces directly. It's a bit complicated as you need to intensity normalize and register the hires volume to the surfaces first. I have an example script if anyone is interested, but no one has used it yet but me I don't think (unless Matt Glasser has gotten his version working, which on second thought he probably has) On Mon, 14 May 2012, Michael Waskom wrote: Hi Bruce, Is there a flag for this on recon-all? Or do you need to use mri_make_surfaces directly? Best, Michael On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Joshua yes, we already have upgraded mris_make_surfaces to take higher res data and refine the surfaces with it. Haven't tried it on the aseg yet, but if you upload a sample dataset I could see how hard it is. cheers Bruce On Mon, 14 May 2012, Joshua Lee wrote: Dear Freesurfers, Over the last years, MR imaging technology hasimproved such that sub 1-mm isotropic scans can be obtained with good signal to noise characteristics. For example, our lab uses 0.7mm isotropic structural MR images. I understand that the Freesurfer pipeline will up-sample these to 1mm isotropic, but it seems a shame that so much information is left unused which could be used to improve the accuracy of sub-cortical and cortical segmentation. My question is whether there are any plans at Freesurfer to change the reference standard resolution from 1mm isotropic, or provide another solution that can help researchers make the most of your technology. Sincerely, Joshua - Joshua ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] average lGI for each subject's hemipshere
Dear all, How can I obtain an average lGI for each subject's hemipshere? I've tried: mris_anatomical_stats -mgz -f lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label/ lgi.annot.ctab -t pial_lgi $SUBJECT lh but I had the following error: ERROR: stating file .../label/lh.aparc.annot It calculates the lgi for each gyri label but it does not give average values for the hemisphere. Thanks a lot. ines ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_robust_template
Dear all, For a longitudinal analysis I need to have within subject templates. After some preprocessing that included FSL's BET, and linear registration of all time points to time-point 1, I fed images to mri_robust_template: mri_robust_template --mov tp1 tp2 tp3 --template template_address --satit It runs fine for some subjects, however I get the following error for some others: ERROR: All entries are zero! Images do not overlap (anymore?). This can have several reasons (i.e. different modalities, different intensity scales, large non-linearities, too diff. voxel sizes ...) Maybe use --transform init.lta with an approx. alignment obtained from tkregister or another registration program. Or do some prior intensity correction? I have rechecked data, they are bias corrected, and coregistered. Any thoughts of what could possibly go wrong here? All the best, Arman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] average lGI for each subject's hemipshere
That looks right. You can also run something like: mri_segstats --slabel subject lh ../label/lh.cortex.label --in lh.thickness --sum sum.dat --id 1 The output is sum.dat doug On 05/15/2012 02:14 PM, Inês Violante wrote: I think I got it, but it would be great if someone could tell me if this is wright: mris_anatomical_stats -l lh.cortex.label -t lh.pial_lgi -log file.txt SUBJECT lh pial thanks, ines On Tue, May 15, 2012 at 6:58 PM, Inês Violanteinesviola...@gmail.com wrote: Dear all, How can I obtain an average lGI for each subject's hemipshere? I've tried: mris_anatomical_stats -mgz -f lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label/ lgi.annot.ctab -t pial_lgi $SUBJECT lh but I had the following error: ERROR: stating file .../label/lh.aparc.annot It calculates the lgi for each gyri label but it does not give average values for the hemisphere. Thanks a lot. ines ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_segstats for T2-relaxation time data?
Dear Freesurfer Folks, I have returned to the problem of trying to extract T2 values from a T2-map using aseg mri_segstats. When I attempt mri_segstats it only returns a small subset of the regions from aseg (see attached file). I would like to attach the T2 map but the file exceeds the 25mb limit for gmail (could I drop the file somewhere?) Could the T2 values need to be in a special format? Thanks very much for your help. Carl On Thu, Dec 30, 2010 at 6:06 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu mailto:ni...@nmr.mgh.harvard.edu wrote: mri_segstats, for example: mri_segstats --seg aseg.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i T1.mgz \ --sum T1.stats produces a text file 'T1.stats' which has stats on each aseg struct as taken from the vol T1.mgz. n. On Thu, 2010-12-30 at 17:52 -0500, Carl Anderson wrote: Dear Freesurfer, I have co-registered a map of whole brain T2-relaxation time values to the corresponding aseg.mgz for this subject (see attached jpegs). Does a tool exist in freesurfer to enable regional sampling of T2 values from the T2-relaxation time map based on aseg? Thanks for any thoughts. -- •~~•~~•~~•~~•~~•~~•~~• Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfr...@gmail.com; carl_ander...@hms.harvard.edu •~~•~~•~~•~~•~~•~~•~~• T2.stats_flirt Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_segstats for T2-relaxation time data?
Hi Carl, you can ftp it or filedrop it (both are detailed on the fs wiki site) cheers Bruce On Tue, 15 May 2012, Carl Anderson wrote: Dear Freesurfer Folks, I have returned to the problem of trying to extract T2 values from a T2-map using aseg mri_segstats. When I attempt mri_segstats it only returns a small subset of the regions from aseg (see attached file). I would like to attach the T2 map but the file exceeds the 25mb limit for gmail (could I drop the file somewhere?) Could the T2 values need to be in a special format? Thanks very much for your help. Carl On Thu, Dec 30, 2010 at 6:06 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu mailto:ni...@nmr.mgh.harvard.edu wrote: mri_segstats, for example: mri_segstats --seg aseg.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i T1.mgz \ --sum T1.stats produces a text file 'T1.stats' which has stats on each aseg struct as taken from the vol T1.mgz. n. On Thu, 2010-12-30 at 17:52 -0500, Carl Anderson wrote: Dear Freesurfer, I have co-registered a map of whole brain T2-relaxation time values to the corresponding aseg.mgz for this subject (see attached jpegs). Does a tool exist in freesurfer to enable regional sampling of T2 values from the T2-relaxation time map based on aseg? Thanks for any thoughts. -- ?~~?~~?~~?~~?~~?~~?~~? Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfr...@gmail.com; carl_ander...@hms.harvard.edu ?~~?~~?~~?~~?~~?~~?~~? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_segstats for T2-relaxation time data?
p.s. what format is the attachment? It doesn't have an extension On Tue, 15 May 2012, Carl Anderson wrote: Dear Freesurfer Folks, I have returned to the problem of trying to extract T2 values from a T2-map using aseg mri_segstats. When I attempt mri_segstats it only returns a small subset of the regions from aseg (see attached file). I would like to attach the T2 map but the file exceeds the 25mb limit for gmail (could I drop the file somewhere?) Could the T2 values need to be in a special format? Thanks very much for your help. Carl On Thu, Dec 30, 2010 at 6:06 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu mailto:ni...@nmr.mgh.harvard.edu wrote: mri_segstats, for example: mri_segstats --seg aseg.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i T1.mgz \ --sum T1.stats produces a text file 'T1.stats' which has stats on each aseg struct as taken from the vol T1.mgz. n. On Thu, 2010-12-30 at 17:52 -0500, Carl Anderson wrote: Dear Freesurfer, I have co-registered a map of whole brain T2-relaxation time values to the corresponding aseg.mgz for this subject (see attached jpegs). Does a tool exist in freesurfer to enable regional sampling of T2 values from the T2-relaxation time map based on aseg? Thanks for any thoughts. -- ?~~?~~?~~?~~?~~?~~?~~? Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfr...@gmail.com; carl_ander...@hms.harvard.edu ?~~?~~?~~?~~?~~?~~?~~? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_segstats for T2-relaxation time data?
Hi Carl, those are all that are in the aseg.mgz. What more did you expect? doug On 05/15/2012 03:44 PM, Carl Anderson wrote: Dear Freesurfer Folks, I have returned to the problem of trying to extract T2 values from a T2-map using aseg mri_segstats. When I attempt mri_segstats it only returns a small subset of the regions from aseg (see attached file). I would like to attach the T2 map but the file exceeds the 25mb limit for gmail (could I drop the file somewhere?) Could the T2 values need to be in a special format? Thanks very much for your help. Carl On Thu, Dec 30, 2010 at 6:06 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu mailto:ni...@nmr.mgh.harvard.edu mailto:ni...@nmr.mgh.harvard.edu mailto:ni...@nmr.mgh.harvard.edu wrote: mri_segstats, for example: mri_segstats --seg aseg.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i T1.mgz \ --sum T1.stats produces a text file 'T1.stats' which has stats on each aseg struct as taken from the vol T1.mgz. n. On Thu, 2010-12-30 at 17:52 -0500, Carl Anderson wrote: Dear Freesurfer, I have co-registered a map of whole brain T2-relaxation time values to the corresponding aseg.mgz for this subject (see attached jpegs). Does a tool exist in freesurfer to enable regional sampling of T2 values from the T2-relaxation time map based on aseg? Thanks for any thoughts. -- •~~•~~•~~•~~•~~•~~•~~• Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfr...@gmail.com mailto:remfr...@gmail.com; carl_ander...@hms.harvard.edu mailto:carl_ander...@hms.harvard.edu •~~•~~•~~•~~•~~•~~•~~• ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] qdec.table.dat file
Hi Freesurfer experts, A newbie question regarding working with QDEC. When I try to upload the qdec.table.dat file (attached) an error messages pops up Error loading the data table. To the best of my knowledge I've followed the guidelines on the tutorial in terms of formatting. What would be your suggestions to troubleshoot this? Thanks! Fidel qdec.table.dat Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] qdec.table.dat file
The last line does not end in a new line. Open it in your text editor, go to the last line, hit return, save it, and try again. doug On 05/15/2012 05:15 PM, Fidel Vila wrote: Hi Freesurfer experts, A newbie question regarding working with QDEC. When I try to upload the qdec.table.dat file (attached) an error messages pops up Error loading the data table. To the best of my knowledge I've followed the guidelines on the tutorial in terms of formatting. What would be your suggestions to troubleshoot this? Thanks! Fidel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] asegstats2table error
Hello, I am trying to get the asegmentation information after the recon-all run in the table form, but I am continuously getting the following error asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas volume --tablefile asegstats.txt SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files ERROR: The stats file /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files I did try to use the skip option , but then , it skips all the files giving the same error. When I individually open the aseg files from the stats folder, those look fine to me. Please advise. Rashmi. This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] asegstats2table error
Do those files exist? Do they have content in them? doug On 05/15/2012 05:51 PM, Rashmi Singh wrote: Hello, I am trying to get the asegmentation information after the recon-all run in the table form, but I am continuously getting the following error asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas volume --tablefile asegstats.txt SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files ERROR: The stats file /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files I did try to use the skip option , but then , it skips all the files giving the same error. When I individually open the aseg files from the stats folder, those look fine to me. Please advise. Rashmi. This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] vertex-wise correlation
Dear Freesurfer experts, I have fMRI data that are processed in AFNI that I would like to examine the relationship with cortical thickness measures. In particular, I am interested in vertex-wise correlation of thickness and BOLD % signal change. The problem is I am new to Freesurfer. So far I have found that the program mri_glmfit appears to be able to handle vertex-wise regressor, with the -pvr option. First, does this enable me to do vertex-wise bivariate correlation? Second, if so, it appears that the input files need to be concatenated (or stacked??), and for FreeSurfer measures, mris_preproc seems to take care of it. But, how can I stack/concatenate the afni-generated files (which are registered to and mapped on to each individual's surface that are in .mgh format)?? I appreciate any input you may have- -- Nobuko Kemmotsu, Ph.D. University of California, San Diego ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
