Re: [Freesurfer] permission denied
It does not work. This is really strange On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote: I beleive it should have a lower case X, as in: chmod -R a+x freesurfer/bin -Zeke On 10/28/2014 01:19 AM, Ali Radaideh wrote: Dear Douglas Thanks for your reply. unfortunatey I still get the same error. Here is the terminal output. Is there anything else I can do? freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl imaging@imaging-ThinkCentre-23:~$ tcsh imaging-ThinkCentre-23:~ tkmedit /usr/local/freesurfer/bin/tkmedit: Permission denied. imaging-ThinkCentre-23:~ On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Try chmod -R a+X freesurfer/bin On 10/26/14 1:57 PM, Ali Radaideh wrote: Dear FreeSurfer users, I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I try a command such such as tkmedit i get the following error /usr/local/freesurfer/bin/tkmedit: permission denied. I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer but did not work. Any ideas why is this happening although I have done the same thing to other PCs and they are working fine. Thanks in advance, Ali -- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 390 ext.5422, 5355, 5364 Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ ___ 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 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. -- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 390 ext.5422, 5355, 5364 Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ ___ 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 -- *Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 390 ext.5422, 5355, 5364Email: ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=* ___ 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] Error with asegstats2table function
Hello Freesurfer Experts, Thanks so much again for all of your help. I am trying to complete the Anatomical ROI Analysis Tutorial because I will need to use segmentation volumes for an experiment we`re running in the lab. In particular, I am trying to complete the group stats files part of the tutorial so that I know how to export this data in the future to excel for statistical analysis. However, I keep getting the following error: IOError: [Errno 13] Permission denied: 'aseg_stats.txt' I have tried to put in my password with sudo, make myself a superuser, and chmod, but nothing seems to work. When I do sudo it will tell me that my SUBJECTS_DIR isn`t defined although it is defined in the first two lines of every terminal window I open (because of my .profile). See here: IOError: [Errno 13] Permission denied: 'aseg_stats.txt' [dbm079-066:/Applications/freesurfer/subjects] claire% sudo asegstats2table --subjects 004 008 --meas volume --tablefile aseg_stats.txt Password: ERROR: SUBJECTS_DIR environment variable not defined! Additionally, sometimes I will also see the following error ERROR: output table name should be specified (use --tablefile FILE) after putting in the following: claire% asegstats2table --subjects 004 008 \ --segno 11 17 18 \ --tablefile aseg.vol.txt ERROR: output table name should be specified (use --tablefile FILE) Please help! I have tried everything I can think of. Thank you for everything, Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot* ___ 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] adding insula voxels
Hi Adam underestimated the insula in the aseg or in the surfaces? cheers Bruce On Wed, 29 Oct 2014, Adam Mezher wrote: Hi Bruce, Sorry for not clarifying. A number of subjects in our set have underestimated insula (usually anatomical right insula but sometimes both). I just uploaded an example to the ftp. I don’t think control points or wm edits can help with some of these so I wanted to see how we could go about editing them manually by adding the correct label to the empty voxels with the Edit Segmentation tool in tkmedit. Thank you, Adam ___ 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] Name external disk not recognized
Dear Freesurfers, Not sure if my question is at the right place here but I'll give it a try. I have a memory disk with white spaces in the name: Seagate Expansion Drive. There is no simple way to rename the disk on my Linux machine. In Unix shell scripting problems with finding the directory can be prevented by putting the whole name in quotation marks, e.g., f1=”Seagate Expansion Drive” and then after that calling f1 with quotation marks (e.g., cp “$f1”/file.xxx /destination/ ). However, if I want to use bbregister then it does not recognize the quotation marks. For example, behind the flag --reg /”$f1”/fsreg.dat Freesurfer tells me that it does not recognize “Expansion” as a flag (probably because it still reads the white space in the name). I was wondering if there is any simple solution around or if the only option seems to try to rename the disk. Best, Ruthger ___ 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] Venous system on 3D models
You can also use bbregister to register the CT to the anatomical. I'm not sure what steps beyond that you'd need to do. doug On 10/29/14 10:47 PM, Zachary Greenberg wrote: Rich, You need SPM preferably (http://www.fil.ion.ucl.ac.uk/spm/) for matlab, and freesurfer. First run recon-all on the patients T1 (after acpc aligning in Spm). Then take the resultant orig.mgz file (convert to .nii using mri_convert orig.mgz orig.nii), and corregister the post-op CT to it using SPM's normalized mutual info. routine. To do this: 1.) open matlab, 2.)type spm at the prompt, 3.) chose fMRI from the gui pop up, 4.) pick corregister (est. and write) from the top left of the spm gui. Then chose the Orig.nii as the reference image, and the patients pos-op CT as the target. Open the corregisterd CT (rCT.nii), the Orig.nii, and pial surface in freeview. Click on each electrode in the CT, and copy the xyz coords from the bottom left into a text file or matlab matrix (it will list the surface RAS coords in bottem left of freeview, which is what you want to display on the freesurfer pial surface). Let me know when you get that far and I'll send you a link to some code that will help you visualize the pial surface with overlaid electrodes. -zack On Wed, Oct 29, 2014 at 7:28 PM, rwlod...@uic.edu mailto:rwlod...@uic.edu rwlod...@uic.edu mailto:rwlod...@uic.edu wrote: I have some post-op CT's for some of my patients but not all, do you have a link or could you explain how to coregister so I can do it for the ones I have? Thank you! On Wed, October 29, 2014 9:18 pm, Zachary Greenberg wrote: Hi Rich, Do you have a post-operative CT scan of your ECoG patient? If you have that and a high-res T1, you can get very accurate reconstruction of electrode positions on the brain surface by corregistering the two. -zack On Wed, Oct 29, 2014 at 3:32 PM, rwlod...@uic.edu mailto:rwlod...@uic.edu rwlod...@uic.edu mailto:rwlod...@uic.edu wrote: Hello my names Rich. I am working on a project that involves creating 3D models of patient brains and placing ECoG (Electrocorticography) leads on these models. I have intra-operative pictures of the leads placed on the subjects and I'm using these pictures to attempt to accurately place the leads. However, as you might guess, the 3D models are very different from looking at a live brain and the true sulcal and gyral pattern is difficult to determine from the pictures. I was wondering if it is possible to have freesurfer create or mark, in some way, the veins on the models so that I can use the venous system as points of reference when placing the leads. If not, is there a better way to do so that you can think of? I am relatively new to freesurfer so I don't fully understand its capability yet. Thanks!! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. -- *Zachary Greenberg* *Assistant Imaging Specialist* *Department of Neurological Surgery* *University of California, San Francisco* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Name external disk not recognized
can you make a symbolic link (ln -s) to the disk and then reference the symlink instead of the direct path? On 10/30/14 10:33 AM, Righart, Ruthger wrote: Dear Freesurfers, Not sure if my question is at the right place here but I'll give it a try. I have a memory disk with white spaces in the name: Seagate Expansion Drive. There is no simple way to rename the disk on my Linux machine. In Unix shell scripting problems with finding the directory can be prevented by putting the whole name in quotation marks, e.g., f1=”Seagate Expansion Drive” and then after that calling f1 with quotation marks (e.g., cp “$f1”/file.xxx /destination/ ). However, if I want to use bbregister then it does not recognize the quotation marks. For example, behind the flag --reg /”$f1”/fsreg.dat Freesurfer tells me that it does not recognize “Expansion” as a flag (probably because it still reads the white space in the name). I was wondering if there is any simple solution around or if the only option seems to try to rename the disk. Best, Ruthger ___ 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] Name external disk not recognized
Cheap solution, use backticks to evaluate the string, e.g. --reg /`echo $f1`/fsreg.dat On 30.10.2014 15:33, Righart, Ruthger wrote: Dear Freesurfers, Not sure if my question is at the right place here but I'll give it a try. I have a memory disk with white spaces in the name: Seagate Expansion Drive. There is no simple way to rename the disk on my Linux machine. In Unix shell scripting problems with finding the directory can be prevented by putting the whole name in quotation marks, e.g., f1=Seagate Expansion Drive and then after that calling f1 with quotation marks (e.g., cp $f1/file.xxx /destination/ ). However, if I want to use bbregister then it does not recognize the quotation marks. For example, behind the flag --reg /$f1/fsreg.dat Freesurfer tells me that it does not recognize Expansion as a flag (probably because it still reads the white space in the name). I was wondering if there is any simple solution around or if the only option seems to try to rename the disk. Best, Ruthger ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [1] 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 [2] . 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. Links: -- [1] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [2] http://www.partners.org/complianceline ___ 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] Name external disk not recognized
Yes, works!!! Thank you Ruthger Righart Le 2014-10-30 15:36, Douglas Greve a écrit : can you make a symbolic link (ln -s) to the disk and then reference the symlink instead of the direct path? On 10/30/14 10:33 AM, Righart, Ruthger wrote: Dear Freesurfers, Not sure if my question is at the right place here but I'll give it a try. I have a memory disk with white spaces in the name: Seagate Expansion Drive. There is no simple way to rename the disk on my Linux machine. In Unix shell scripting problems with finding the directory can be prevented by putting the whole name in quotation marks, e.g., f1=”Seagate Expansion Drive” and then after that calling f1 with quotation marks (e.g., cp “$f1”/file.xxx /destination/ ). However, if I want to use bbregister then it does not recognize the quotation marks. For example, behind the flag --reg /”$f1”/fsreg.dat Freesurfer tells me that it does not recognize “Expansion” as a flag (probably because it still reads the white space in the name). I was wondering if there is any simple solution around or if the only option seems to try to rename the disk. Best, Ruthger ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] permission denied
Ali,
First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are
working properly? I am under the impression that versions of freesurfer
pre-version 5.3 will not work on newer linux distributions?
In regards to your current permision denied issue... What happens if you
try and run tkmedit as root user? Also, you not using virtual machine
setup are you?
-Zeke
On 10/30/2014 06:27 AM, Ali Radaideh wrote:
It does not work. This is really strange
On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu
mailto:zkauf...@nmr.mgh.harvard.edu wrote:
I beleive it should have a lower case X, as in:
chmod -R a+x freesurfer/bin
-Zeke
On 10/28/2014 01:19 AM, Ali Radaideh wrote:
Dear Douglas
Thanks for your reply. unfortunatey I still get the same error.
Here is
the terminal output. Is there anything else I can do?
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer/subjects
MNI_DIR /usr/local/freesurfer/mni
FSL_DIR /usr/local/fsl
imaging@imaging-ThinkCentre-23:~$ tcsh
imaging-ThinkCentre-23:~ tkmedit
/usr/local/freesurfer/bin/tkmedit: Permission denied.
imaging-ThinkCentre-23:~
On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
Try chmod -R a+X freesurfer/bin
On 10/26/14 1:57 PM, Ali Radaideh wrote:
Dear FreeSurfer users,
I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One
of the
PCs has the latest version of freesurfer 5.3.0 while the others
have the version 5.0.0. The PC that is installed with the latest
version freesurfer 5.3.0 does not allow me to run any
command and
everytime I try a command such such as tkmedit i get the
following
error
/usr/local/freesurfer/bin/tkmedit: permission denied.
I have tried to change the permission settings
sudo chown -R imaging:imaging freesurfer
but did not work.
Any ideas why is this happening although I have done the same
thing to other PCs and they are working fine.
Thanks in advance,
Ali
--
/Ali M. Al-Radaideh. PhD
Assistant Professor
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo
mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
mailto:ali.radai...@hu.edu.jo
/
/webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
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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.
--
/Ali M. Al-Radaideh. PhD
Assistant Professor
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
/
/webpage:
Re: [Freesurfer] Unknown problem with fsgd file
The problem is that the class name exceeds the maximum number of characters. For some strange reason I set that to be 50 and the class name is 55. I've changed it in our code tree, but you'll just have to shorten the name and it should work. doug On 10/29/2014 07:15 PM, Bronwyn Overs wrote: Dear Freesurfer Mailing list, I have been attempting to run mri_glmfit using a complicated fsgd file (1 categorical varible with 5 levels, 3 categorical variables with 2 levels, age as covariate). When I run the command, I receive the following error: gdfReadHeader: reading site-gender-group-riskhaplotype.fsgd Input line 5, subjid = 100121, class siteMelbourne-anyRiskAnyRisk-genderFemale-groupControl not defined FSGDF Format Error: file = site-gender-group-riskhaplotype.fsgd, tag=Input I have double checked the fsgd file and confirmed that the class for participant 100121 was specific correctly at the beginning of the file (correct spelling and case was used). So I cannot identify the source of the error. Can you advise me as to what may be going wrong? My full fsgd file begins like this (I have 389 subjects but have provided only the first 20 for brevity): GroupDescriptorFile 1 Title GLM_SiteGender Class siteBrisbane-anyProtNoProt-genderMale-groupCase Class siteBrisbane-anyProtNoProt-genderFemale-groupCase Class siteBrisbane-anyProtNoProt-genderMale-groupControl Class siteBrisbane-anyProtNoProt-genderFemale-groupControl Class siteBrisbane-anyProtAnyProt-genderMale-groupCase Class siteBrisbane-anyProtAnyProt-genderFemale-groupCase Class siteBrisbane-anyProtAnyProt-genderMale-groupControl Class siteBrisbane-anyProtAnyProt-genderFemale-groupControl Class siteMelbourne-anyProtNoProt-genderMale-groupCase Class siteMelbourne-anyProtNoProt-genderFemale-groupCase Class siteMelbourne-anyProtNoProt-genderMale-groupControl Class siteMelbourne-anyProtNoProt-genderFemale-groupControl Class siteMelbourne-anyProtAnyProt-genderMale-groupCase Class siteMelbourne-anyProtAnyProt-genderFemale-groupCase Class siteMelbourne-anyProtAnyProt-genderMale-groupControl Class siteMelbourne-anyProtAnyProt-genderFemale-groupControl Class siteNewcastle-anyProtNoProt-genderMale-groupCase Class siteNewcastle-anyProtNoProt-genderFemale-groupCase Class siteNewcastle-anyProtNoProt-genderMale-groupControl Class siteNewcastle-anyProtNoProt-genderFemale-groupControl Class siteNewcastle-anyProtAnyProt-genderMale-groupCase Class siteNewcastle-anyProtAnyProt-genderFemale-groupCase Class siteNewcastle-anyProtAnyProt-genderMale-groupControl Class siteNewcastle-anyProtAnyProt-genderFemale-groupControl Class sitePerth-anyProtNoProt-genderMale-groupCase Class sitePerth-anyProtNoProt-genderFemale-groupCase Class sitePerth-anyProtNoProt-genderMale-groupControl Class sitePerth-anyProtNoProt-genderFemale-groupControl Class sitePerth-anyProtAnyProt-genderMale-groupCase Class sitePerth-anyProtAnyProt-genderFemale-groupCase Class sitePerth-anyProtAnyProt-genderMale-groupControl Class sitePerth-anyProtAnyProt-genderFemale-groupControl Class siteSydney-anyProtNoProt-genderMale-groupCase Class siteSydney-anyProtNoProt-genderFemale-groupCase Class siteSydney-anyProtNoProt-genderMale-groupControl Class siteSydney-anyProtNoProt-genderFemale-groupControl Class siteSydney-anyProtAnyProt-genderMale-groupCase Class siteSydney-anyProtAnyProt-genderFemale-groupCase Class siteSydney-anyProtAnyProt-genderMale-groupControl Class siteSydney-anyProtAnyProt-genderFemale-groupControl Variables age Input 100105SA sitePerth-anyProtNoProt-genderMale-groupCase 23 Input 100112SA siteBrisbane-anyProtAnyProt-genderMale-groupCase 22 Input 100117SA siteBrisbane-anyProtNoProt-genderMale-groupCase 39 Input 100118 siteBrisbane-anyProtNoProt-genderFemale-groupCase 30 Input 100121 siteMelbourne-anyProtAnyProt-genderFemale-groupControl 21 Input 100122 siteMelbourne-anyProtAnyProt-genderMale-groupControl 53 Input 100151 siteMelbourne-anyProtNoProt-genderFemale-groupControl 58 Input 100185SA siteBrisbane-anyProtNoProt-genderFemale-groupControl 24 Input 100187 siteBrisbane-anyProtNoProt-genderMale-groupCase 24 Input 100189 siteBrisbane-anyProtNoProt-genderFemale-groupCase 21 Input 100190 siteSydney-anyProtNoProt-genderMale-groupControl 41 Input 100191 siteMelbourne-anyProtAnyProt-genderFemale-groupControl 19 Input 100193SA siteSydney-anyProtNoProt-genderMale-groupControl 26 Input 100196 siteBrisbane-anyProtNoProt-genderMale-groupControl 55 Input 100197SA siteBrisbane-anyProtNoProt-genderFemale-groupCase 30 Input 100200SA siteBrisbane-anyProtNoProt-genderMale-groupControl 39 Input 100204 siteSydney-anyProtAnyProt-genderFemale-groupControl 50 Input 100208 siteBrisbane-anyProtNoProt-genderMale-groupControl 25 Input 100209SA siteBrisbane-anyProtAnyProt-genderMale-groupCase 35 Input 100214 siteSydney-anyProtAnyProt-genderMale-groupCase 44 The mri_glmfit command I am using is as follows: mri_glmfit --y
Re: [Freesurfer] permission denied
Try this chmod -R a+x freesurfer/bin/* On 10/30/2014 06:27 AM, Ali Radaideh wrote: It does not work. This is really strange On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: I beleive it should have a lower case X, as in: chmod -R a+x freesurfer/bin -Zeke On 10/28/2014 01:19 AM, Ali Radaideh wrote: Dear Douglas Thanks for your reply. unfortunatey I still get the same error. Here is the terminal output. Is there anything else I can do? freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl imaging@imaging-ThinkCentre-23:~$ tcsh imaging-ThinkCentre-23:~ tkmedit /usr/local/freesurfer/bin/tkmedit: Permission denied. imaging-ThinkCentre-23:~ On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Try chmod -R a+X freesurfer/bin On 10/26/14 1:57 PM, Ali Radaideh wrote: Dear FreeSurfer users, I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I try a command such such as tkmedit i get the following error /usr/local/freesurfer/bin/tkmedit: permission denied. I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer but did not work. Any ideas why is this happening although I have done the same thing to other PCs and they are working fine. Thanks in advance, Ali -- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 390 ext.5422, 5355, 5364 Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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. -- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 390 ext.5422, 5355, 5364 Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ ___ 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 -- /Ali M. Al-Radaideh. PhD Assistant Professor Head ofDepartment of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite
Re: [Freesurfer] Error with asegstats2table function
You are in a folder that you do not have write permission to. Try cding to a different folder, or spec a path to a folder where you have write permissions, eg, asegstats2table --subjects 004 008 --meas volume --tablefile /tmp/aseg_stats.txt doug On 10/30/2014 08:28 AM, Claire Morley wrote: Hello Freesurfer Experts, Thanks so much again for all of your help. I am trying to complete the Anatomical ROI Analysis Tutorial because I will need to use segmentation volumes for an experiment we`re running in the lab. In particular, I am trying to complete the group stats files part of the tutorial so that I know how to export this data in the future to excel for statistical analysis. However, I keep getting the following error: IOError: [Errno 13] Permission denied: 'aseg_stats.txt' I have tried to put in my password with sudo, make myself a superuser, and chmod, but nothing seems to work. When I do sudo it will tell me that my SUBJECTS_DIR isn`t defined although it is defined in the first two lines of every terminal window I open (because of my .profile). See here: IOError: [Errno 13] Permission denied: 'aseg_stats.txt' [dbm079-066:/Applications/freesurfer/subjects] claire% sudo asegstats2table --subjects 004 008 --meas volume --tablefile aseg_stats.txt Password: ERROR: SUBJECTS_DIR environment variable not defined! Additionally, sometimes I will also see the following error ERROR: output table name should be specified (use --tablefile FILE) after putting in the following: claire% asegstats2table --subjects 004 008 \ --segno 11 17 18 \ --tablefile aseg.vol.txt ERROR: output table name should be specified (use --tablefile FILE) Please help! I have tried everything I can think of. Thank you for everything, Claire -- /We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot/ ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Fwd:
Notification of the “Isaac Peral” Program to contract one senior researcher associated with BBVA Foundation-UPM Industry-Academia chairs for scientific-technological research in Medical Imaging, within Marie Curie Action COFUND. This notice provides for a maximum of one position in the area of scientific-technological initiatives in Biotech indicated below, in accordance with the procedure established in the Regulatory Bases of 30 April 2009 for the ISAAC PERAL Program for Senior UPM Researchers (in the attached document). The candidate degree may be from any specialization in Engineering, Physics, Mathematics, Statistics, Biology, Biochemistry, etc. Location: The activities will be carried out in the Campus of International Excellence: Campus of Montegancedo at the CTB: Centre for Biomedical Technology (www.ctb.upm.es), in Madrid, Spain. Beneficiaries: 1. Have held a PhD for more than 10 years, effectively pursuing uninterrupted research activity during that time. 2. Have extensive research experience in the sphere of the profile of the contract announced, i.e. biomedical imaging. 3. Have pursued their research activity following the award of their PhD in relevant foreign Research Centers for at least six years or have studied the whole of the PhD and graduated in a foreign University or Research Centre and have pursued subsequent research activity in a relevant foreign research center for at least three years. 4. Have certified experience in the management of research groups in university institutions or relevant research centers. All the requirements demanded and the merits argued by candidates must have been fulfilled prior to the date of termination of the period for the submission of applications. Conditions of the position: 1. Gross remuneration shall not be less than 8 € nor more than 9 € per year. 2. Three year contracts for two young PhDs 3. Three positions for PhD studies (four years) 4. A 3 € support for the Senior researcher during the first year of contract to facilitate the start of the research activities 5. A minimum of 100m2 space available in the Centre for Biomedical Technology N.B.: All the the details of the call can be consulted at the following link: *http://www.upm.es/sfs/Rectorado/Vicerrectorado%20de%20Investigacion/Servicio%20de%20Investigacion/Ayudas_y_Convocatorias/Convocatorias_Propias/Convocatoria-MedImaging-Eng.pdf http://www.upm.es/sfs/Rectorado/Vicerrectorado%20de%20Investigacion/Servicio%20de%20Investigacion/Ayudas_y_Convocatorias/Convocatorias_Propias/Convocatoria-MedImaging-Eng.pdf* Interested candidates should send CV to the following email address francisco.delp...@ctb.upm.es. [image: http://www.upm.es/sfs/Montegancedo/Noticias/imagenes/ctb.gif] Prof. Francisco del Pozo Director Center for Biomedical Technology (CTB) Universidad Politécnica de Madrid Parque Científico y Tecnológico de la UPM Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, ES Tfo: +34 913364632 (Tfo: +34 913364631) www.ctb.upm.es ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Senior Researcher position in Madrid, Spain
Notification of the “Isaac Peral” Program to contract one senior researcher associated with BBVA Foundation-UPM Industry-Academia chairs for scientific-technological research in Medical Imaging, within Marie Curie Action COFUND. This notice provides for a maximum of one position in the area of scientific-technological initiatives in Biotech indicated below, in accordance with the procedure established in the Regulatory Bases of 30 April 2009 for the ISAAC PERAL Program for Senior UPM Researchers (in the attached document). The candidate degree may be from any specialization in Engineering, Physics, Mathematics, Statistics, Biology, Biochemistry, etc. Location: The activities will be carried out in the Campus of International Excellence: Campus of Montegancedo at the CTB: Centre for Biomedical Technology (www.ctb.upm.es), in Madrid, Spain. Beneficiaries: 1. Have held a PhD for more than 10 years, effectively pursuing uninterrupted research activity during that time. 2. Have extensive research experience in the sphere of the profile of the contract announced, i.e. biomedical imaging. 3. Have pursued their research activity following the award of their PhD in relevant foreign Research Centers for at least six years or have studied the whole of the PhD and graduated in a foreign University or Research Centre and have pursued subsequent research activity in a relevant foreign research center for at least three years. 4. Have certified experience in the management of research groups in university institutions or relevant research centers. All the requirements demanded and the merits argued by candidates must have been fulfilled prior to the date of termination of the period for the submission of applications. Conditions of the position: 1. Gross remuneration shall not be less than 8 € nor more than 9 € per year. 2. Three year contracts for two young PhDs 3. Three positions for PhD studies (four years) 4. A 3 € support for the Senior researcher during the first year of contract to facilitate the start of the research activities 5. A minimum of 100m2 space available in the Centre for Biomedical Technology N.B.: All the the details of the call can be consulted at the following link: *http://www.upm.es/sfs/Rectorado/Vicerrectorado%20de%20Investigacion/Servicio%20de%20Investigacion/Ayudas_y_Convocatorias/Convocatorias_Propias/Convocatoria-MedImaging-Eng.pdf http://www.upm.es/sfs/Rectorado/Vicerrectorado%20de%20Investigacion/Servicio%20de%20Investigacion/Ayudas_y_Convocatorias/Convocatorias_Propias/Convocatoria-MedImaging-Eng.pdf* Interested candidates should send CV to the following email address francisco.delp...@ctb.upm.es. [image: http://www.upm.es/sfs/Montegancedo/Noticias/imagenes/ctb.gif] Prof. Francisco del Pozo Director Center for Biomedical Technology (CTB) Universidad Politécnica de Madrid Parque Científico y Tecnológico de la UPM Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, ES Tfo: +34 913364632 (Tfo: +34 913364631) www.ctb.upm.es ___ 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] Longitudinal prediction
Hi Martin, could you please confirm whether the glm analysis was correctly performed ? the command line is:mri_glmfit --glmdir DIR --y lh.thickness-pc1.stack.fwhm15.mgh --label lh.fsaverage.cortex.label --fsgd FSGD_FILE --C Contrast-010..0.mtx --surf fsaverage lh I get results, but I when I do the same command for the analysis from the 2-stage-model webpage, the results are different. For example, on the webpage the cmd is:mri_glmfit --osgm --glmdir DIR --y Y.mgh --label LABEL.label --surf fsaverage lh I tried to receive the same result with:mri_glmfit --glmdir DIR --y Y.mgh --label LABEL.label --fsgd FSGD_FILE --C Contrast-100...0.mtx --surf fsaverage lh but the results are different. In this case, how can I be sure that the first analysis was performed correctly ? the fsgd file was constructed using the base-subjects and the values were taken as in the cross file that is used by qdec. Thanks,Alex On Thursday, October 23, 2014 2:52 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Alex, you are not looking at a one sample group mean (osgd) so don't pass that flag. Your design is probably something like 1 A other_co_vars_to_regress_out (these are column vectors). so contrast in that case would be [ 0 1 0... ] That should create all outputs. All of this is really cross sectional analysis where the depending variable is simply the 'change in thickness' instead of thickness itself. Take a look at the glm tutorial on the wiki, which describes the process. Best, Martin On 10/23/2014 02:40 PM, Alex Hanganu wrote: Hi Martin, thanks for confirming. I duplicated the parameter and got good results in qdec. I also tried to repeat the analysis with mri_glmfit but I can't manage to come to an end. In order to analyse the correlation between pc1 and parameter 'A', it seems that I have to construct an fsgd file, that is different from the .qdec file included in the long_mris_slopes command. Nevertheless, after doing so (presumably all Inputs were attibuted to subject.long.base-time1 and subject.long.base-time2) I thought that a contrast is needed, yet the --C and the --osgm flags cannot be used together. - How can the correlation between -pc1 and parameter 'A' be performed in this case ? Additionally, after performing the mri_glmfit described in the 2-stage-model page, in the tksurfer how can I see the plot ? The y.fsgd file wasn't created. Is there another method ? Thanks, Alex Le mardi 21 octobre 2014 16h40, Martin Reuter mreu...@nmr.mgh.harvard.edu a écrit : Hi Alex, you have to duplicate the parameter (it is basically fixed across time). If you put 0 for tp2, it will average the two values, which is not what you want. Otherwise I think it is the correct approach. Best, Martin On 10/21/2014 04:31 PM, Alex Hanganu wrote: Dear Martin, thank you very much for your answer ! and thanks for all the details ! - yes, we have exactly 2 time points in all subjects and the parameter is a single number. In qdec - it seems that qdec table has to include the parameter 'A' both at time 1 and at time 2 in order for long_qdec_table command to create the cross file. I put a zero at time 2. In qdec design we analyzed parameter 'A' with -pc1 and -spc. I'm not sure that this is the correct approach. I'll continue with LME and mri_glmfit. Sincerely, Alex Le mardi 21 octobre 2014 9h19, Martin Reuter mreu...@nmr.mgh.harvard.edu a écrit : Hi Alex, the parameter is a single number that happens to be measured at time 1 right, eg baseline age? Lets call that parameter 'A' for the discussion below. Also you have exactly 2 time points in all subjects? There is two alternatives: 1. Simple approach (2-stage-model): You compute the atrophy rate (e.g. percent thickness change) on the cortex (long_mris_slopes) for each subject. At this point you have 1 measure per subject and work cross-sectionally. You can use qdec or mri_glmfit to correlate 'A' (independent parameter) with the thickness change (dependent variable). This is OK if you have the same number of time points and the same time distance in all subjects. Details here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel 2. Better approach: use Linear Mixed Effects models (we have matlab tools for that). This model is more flexible (different manycolumn of ones, time points, different time intervals, even subjects with a single time point can be added). You'd setup a system like Y_ij = beta_0 + b_i + beta_1 * A_i + beta_2 t_ij + beta_3 A_i * tij + error_ij where Y_ij is the thickness of subject i at time point j (known) t_ij is the time from baseline of the j measurement in subject i (known), A_i is the variable you measure at baseline in subject i (known), the model will estimate the following: b_i (a random effect) is the subject specific
Re: [Freesurfer] Longitudinal prediction
Hi Alex, the QDEC output (text in the terminal) should have the command line that was used to call the mri_glmfit command. Best, Martin On 10/30/2014 03:08 PM, Alex Hanganu wrote: Hi Martin, could you please confirm whether the glm analysis was correctly performed ? the command line is: /mri_glmfit --glmdir DIR --y lh.thickness-pc1.stack.fwhm15.mgh //--label lh.fsaverage.cortex.label //--fsgd FSGD_FILE --C Contrast-010..0.mtx --surf fsaverage lh / I get results, but I when I do the same command for the analysis from the 2-stage-model webpage, the results are different. For example, on the webpage the cmd is: /mri_glmfit --osgm --glmdir DIR --y Y.mgh --label LABEL.label --surf fsaverage lh/ I tried to receive the same result with: /mri_glmfit --glmdir DIR --y Y.mgh //--label LABEL.label //--fsgd FSGD_FILE --C Contrast-100...0.mtx --surf fsaverage lh / but the results are different. In this case, how can I be sure that the first analysis was performed correctly ? the /fsgd/ file was constructed using the base-subjects and the values were taken as in the /cross/ file that is used by qdec. Thanks, Alex On Thursday, October 23, 2014 2:52 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Alex, you are not looking at a one sample group mean (osgd) so don't pass that flag. Your design is probably something like 1 A other_co_vars_to_regress_out (these are column vectors). so contrast in that case would be [ 0 1 0... ] That should create all outputs. All of this is really cross sectional analysis where the depending variable is simply the 'change in thickness' instead of thickness itself. Take a look at the glm tutorial on the wiki, which describes the process. Best, Martin On 10/23/2014 02:40 PM, Alex Hanganu wrote: Hi Martin, thanks for confirming. I duplicated the parameter and got good results in qdec. I also tried to repeat the analysis with mri_glmfit but I can't manage to come to an end. In order to analyse the correlation between pc1 and parameter 'A', it seems that I have to construct an fsgd file, that is different from the .qdec file included in the long_mris_slopes command. Nevertheless, after doing so (presumably all Inputs were attibuted to subject.long.base-time1 and subject.long.base-time2) I thought that a contrast is needed, yet the --C and the --osgm flags cannot be used together. - How can the correlation between -pc1 and parameter 'A' be performed in this case ? Additionally, after performing the mri_glmfit described in the 2-stage-model page, in the tksurfer how can I see the plot ? The y.fsgd file wasn't created. Is there another method ? Thanks, Alex Le mardi 21 octobre 2014 16h40, Martin Reuter mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu a écrit : Hi Alex, you have to duplicate the parameter (it is basically fixed across time). If you put 0 for tp2, it will average the two values, which is not what you want. Otherwise I think it is the correct approach. Best, Martin On 10/21/2014 04:31 PM, Alex Hanganu wrote: Dear Martin, thank you very much for your answer ! and thanks for all the details ! - yes, we have exactly 2 time points in all subjects and the parameter is a single number. In qdec - it seems that qdec table has to include the parameter 'A' both at time 1 and at time 2 in order for long_qdec_table command to create the cross file. I put a zero at time 2. In qdec design we analyzed parameter 'A' with -pc1 and -spc. I'm not sure that this is the correct approach. I'll continue with LME and mri_glmfit. Sincerely, Alex Le mardi 21 octobre 2014 9h19, Martin Reuter mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu a écrit : Hi Alex, the parameter is a single number that happens to be measured at time 1 right, eg baseline age? Lets call that parameter 'A' for the discussion below. Also you have exactly 2 time points in all subjects? There is two alternatives: 1. Simple approach (2-stage-model): You compute the atrophy rate (e.g. percent thickness change) on the cortex (long_mris_slopes) for each subject. At this point you have 1 measure per subject and work cross-sectionally. You can use qdec or mri_glmfit to correlate 'A' (independent parameter) with the thickness change (dependent variable). This is OK if you have the same number of time points and the same time distance in all subjects. Details here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel 2. Better approach: use Linear Mixed Effects models (we have matlab tools for that). This model is more flexible (different manycolumn of ones, time points, different time intervals, even subjects with a single time point can be added). You'd setup a system like Y_ij = beta_0 + b_i + beta_1 * A_i + beta_2 t_ij + beta_3 A_i * tij + error_ij where Y_ij is the thickness of subject i at time point j (known) t_ij is the time from baseline of the j measurement in
[Freesurfer] Converting lesion volume to surface area
Hello, Previously we have used a lesion of 128 microliters and have filtered out anything smaller in volume than that for analyses (single subject pothole analysis). Now we want to do something similar on the surface. So we need to approximate the surface area of that 128 microliters when translated to group analysis surface (fsaverage). 128 microliters is 128 data points in 1x1x1 resolution. Let's say those data points only exist in the cortical ribbon volume. Question 1: How many of the 128 data points from cortical ribbon volume get translated into surface space? What is the volume to surface translation ratio? Question 2: Because we want to filter clusters with mri_surfcluster, we are interested in the resulting area of our original 128 lesion. Therefore, how much area is represented by each data point when translated onto the surface? Is this simply AvgVtxArea of the inflated surface multiplied by the number of data points that get translated from volume to surface? And what is the best way to answer these two questions from standard Freesurfer output: e.g. Should we calculate from the (NumVert SurfArea GrayVol) columns of the lh.aparc.stats file, get the mean of all SurfArea/GrayVol from aparc.stats, and then multiple by our 128? Any thoughts or suggestions would be appreciated. Thanks, Tim ___ 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] Longitudinal prediction
right ! I totally forgot about this ! Thank you Martin ! Sincerely,Alex On Thursday, October 30, 2014 3:33 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Alex, the QDEC output (text in the terminal) should have the command line that was used to call the mri_glmfit command. Best, Martin On 10/30/2014 03:08 PM, Alex Hanganu wrote: Hi Martin, could you please confirm whether the glm analysis was correctly performed ? the command line is: mri_glmfit --glmdir DIR --y lh.thickness-pc1.stack.fwhm15.mgh --label lh.fsaverage.cortex.label --fsgd FSGD_FILE --C Contrast-010..0.mtx --surf fsaverage lh I get results, but I when I do the same command for the analysis from the 2-stage-model webpage, the results are different. For example, on the webpage the cmd is: mri_glmfit --osgm --glmdir DIR --y Y.mgh --label LABEL.label --surf fsaverage lh I tried to receive the same result with: mri_glmfit --glmdir DIR --y Y.mgh --label LABEL.label --fsgd FSGD_FILE --C Contrast-100...0.mtx --surf fsaverage lh but the results are different. In this case, how can I be sure that the first analysis was performed correctly ? the fsgd file was constructed using the base-subjects and the values were taken as in the cross file that is used by qdec. Thanks, Alex On Thursday, October 23, 2014 2:52 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Alex, you are not looking at a one sample group mean (osgd) so don't pass that flag. Your design is probably something like 1 A other_co_vars_to_regress_out (these are column vectors). so contrast in that case would be [ 0 1 0... ] That should create all outputs. All of this is really cross sectional analysis where the depending variable is simply the 'change in thickness' instead of thickness itself. Take a look at the glm tutorial on the wiki, which describes the process. Best, Martin On 10/23/2014 02:40 PM, Alex Hanganu wrote: Hi Martin, thanks for confirming. I duplicated the parameter and got good results in qdec. I also tried to repeat the analysis with mri_glmfit but I can't manage to come to an end. In order to analyse the correlation between pc1 and parameter 'A', it seems that I have to construct an fsgd file, that is different from the .qdec file included in the long_mris_slopes command. Nevertheless, after doing so (presumably all Inputs were attibuted to subject.long.base-time1 and subject.long.base-time2) I thought that a contrast is needed, yet the --C and the --osgm flags cannot be used together. - How can the correlation between -pc1 and parameter 'A' be performed in this case ? Additionally, after performing the mri_glmfit described in the 2-stage-model page, in the tksurfer how can I see the plot ? The y.fsgd file wasn't created. Is there another method ? Thanks, Alex Le mardi 21 octobre 2014 16h40, Martin Reuter mreu...@nmr.mgh.harvard.edu a écrit : Hi Alex, you have to duplicate the parameter (it is basically fixed across time). If you put 0 for tp2, it will average the two values, which is not what you want. Otherwise I think it is the correct approach. Best, Martin On 10/21/2014 04:31 PM, Alex Hanganu wrote: Dear Martin, thank you very much for your answer ! and thanks for all the details ! - yes, we have exactly 2 time points in all subjects and the parameter is a single number. In qdec - it seems that qdec table has to include the parameter 'A' both at time 1 and at time 2 in order for long_qdec_table command to create the cross file. I put a zero at time 2. In qdec design we analyzed parameter 'A' with -pc1 and -spc. I'm not sure that this is the correct approach. I'll continue with LME and mri_glmfit. Sincerely, Alex Le mardi 21 octobre 2014 9h19, Martin Reuter mreu...@nmr.mgh.harvard.edu a écrit : Hi Alex, the parameter is a single number that happens to be measured at time 1 right, eg baseline age? Lets call that parameter 'A' for the discussion below. Also you have exactly 2 time points in all subjects? There is two alternatives: 1. Simple approach (2-stage-model): You compute the atrophy rate (e.g. percent thickness change) on the cortex (long_mris_slopes) for each subject. At this point you have 1 measure per subject and work cross-sectionally. You can use qdec or mri_glmfit to correlate 'A' (independent parameter) with the thickness change (dependent variable). This is OK if you have the same number of time points and the same time distance in all subjects. Details here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel 2. Better approach: use Linear Mixed Effects models (we have matlab tools for that). This model is more flexible (different manycolumn of ones, time points, different time intervals, even subjects with a single
Re: [Freesurfer] adding insula voxels
I believe it's in the surfaces. It is apparent when I load the lh.pial and lh.white over the brainmask. thanks, Adam ___ 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] adding insula voxels
Can you send us an image? On Oct 30, 2014, at 7:48 PM, Adam Mezher adammez...@gmail.com wrote: I believe it's in the surfaces. It is apparent when I load the lh.pial and lh.white over the brainmask. thanks, Adam ___ 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] adding insula voxels
I uploaded one when I sent the first email, did you receive it? Uploaded to: ftp.nmr.mgh.harvard.edu ; cd transfer/incoming The file was titled ‘mezher_insula_fail.tar.gz’ which contains the entire FS folder for one subject. Should I go ahead and resend it? Thanks!___ 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.
