Re: [Freesurfer] TRACULA: how to implement DTI repeat sequence?
Hi Priti, Thanks so much for your prompt reply! I have specified all our specs like you suggested below. However, I'm a bit confused as I thought this shouldn't be necessary as we feed TRACULA with original GE DICOM files. Doesn't TRACULA read this info from the DICOM headers? Also, it looks like TRACULA assumes that there is only one folder (sequence) per subject. However, as we repeat ours we have 2 per subject meaning I'd like to point to 2 different folders with the 1st image of each defining the sequence like set dcmlist = 014/MRI/AxDTI1/IM-0013-0001.dcm set dcmlist = 014/MRI/AxDTI2/IM-0014-0001.dcm Additionally, I got some errors running trac-preproc with just one series (I include my dmrirc at the end of this message). Any clue where I screw up here? Thanks so much! Ansgar New invocation of trac-preproc ajfurst VALinux1 Linux VALinux1 2.6.35.14-95.fc14.x86_64 #1 SMP Tue Aug 16 21:01:58 UTC 2011 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 1024 total used free sharedbuffers cached Mem: 806273235650844497648 0 1978642413064 -/+ buffers/cache: 9541567108576 Swap: 10158076 2288 10155788 #- /usr/local/freesurfer/bin/trac-preproc #- #@# Image corrections Tue Sep 20 17:10:45 PDT 2011 mri_convert /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz mri_convert /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm... Starting DICOMRead2() dcmfile = /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm dcmdir = /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1 Ref Series No = 13 Found 2032 files, checking for dicoms Found 2030 dicom files in series. First Sorting Computing Slice Direction Vs: 0.051 -0.354 2.4743 Vs: 0.0203999 -0.141599 0.989714 Second Sorting Counting frames nframes = 35 nslices = 58 ndcmfiles = 2030 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=6600.00, TE=84.20, TI=0.00, flip angle=90.00 i_ras = (-0.999791, -0.00289925, -0.0202339) j_ras = (0, -0.989897, 0.141789) k_ras = (-0.0203999, 0.141599, 0.989714) writing to /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz... mri_probedicom --i /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dcminfo.dat cp /home/ajfurst/Data/WRIISC/scripts/30+5gradtable.txt /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvecs cp /home/ajfurst/Data/WRIISC/scripts/bvalfile_1sess.txt /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvals flip4fsl /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2.19727 fslswapdim /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz x -y z /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz INFO: found /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.mghdti.bvecs /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.mghdti.bvals /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvals eddy_correct /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.nii.gz 0 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0001 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0002 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0003 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0004 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0005 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0006 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0007 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0008 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0009 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0010 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0011
Re: [Freesurfer] Problem writing talairach.m3z in mri_ca_register
On Tue, Sep 20, 2011 at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what other information would you like? Can you remind me: are you running on a cluster? Does this happen if you run on your local workstation? Do you have limits on # of open files? Yes, I am running on a cluster with Gentoo (Linux imageserver1 2.6.20-gentoo-r8 #2 SMP Fri May 25 10:23:59 CEST 2007 x86_64 Intel(R) Xeon(R) CPU X5355 @ 2.66GHz GenuineIntel GNU/Linux) I runs without problems on the same data on a MAC The limits in the cluster are: ulimit -a core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 155648 max locked memory (kbytes, -l) 32 max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size(512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 8192 cpu time (seconds, -t) unlimited max user processes (-u) 155648 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited Still haven't resolved the problem. I was wondering, is there some way of forcing mri_ca_register to finish fast (to make error tracing easier)? I have tried using -tol [some large numer], but still it takes many hours before reaching the part where talairach.m3z is written (the part that fails). Best, Lauge ___ 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] TRACULA: how to implement DTI repeat sequence?
Hi Ansgar - Currently there's no way to specify multiple scans for the same subject as dicom files, sorry. You can concatenate the DWIs from the 2 scans in one nifti file, and also concatenate the bvecs/bvals from the two scans, and pass the concatenation to dmrirc. As for your error, it looks like maybe the freesurfer recon wasn't found, so it skipped some steps (diffusion-to-anatomical registration and mask creation). Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist? a.y On Thu, 22 Sep 2011, Ansgar Furst wrote: Hi Priti, Thanks so much for your prompt reply! I have specified all our specs like you suggested below. However, I'm a bit confused as I thought this shouldn't be necessary as we feed TRACULA with original GE DICOM files. Doesn't TRACULA read this info from the DICOM headers? Also, it looks like TRACULA assumes that there is only one folder (sequence) per subject. However, as we repeat ours we have 2 per subject meaning I'd like to point to 2 different folders with the 1st image of each defining the sequence like set dcmlist = 014/MRI/AxDTI1/IM-0013-0001.dcm set dcmlist = 014/MRI/AxDTI2/IM-0014-0001.dcm Additionally, I got some errors running trac-preproc with just one series (I include my dmrirc at the end of this message). Any clue where I screw up here? Thanks so much! Ansgar New invocation of trac-preproc ajfurst VALinux1 Linux VALinux1 2.6.35.14-95.fc14.x86_64 #1 SMP Tue Aug 16 21:01:58 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 8062732 3565084 4497648 0 197864 2413064 -/+ buffers/cache: 954156 7108576 Swap: 10158076 2288 10155788 #- /usr/local/freesurfer/bin/trac-preproc #- #@# Image corrections Tue Sep 20 17:10:45 PDT 2011 mri_convert /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz mri_convert /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm... Starting DICOMRead2() dcmfile = /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm dcmdir = /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1 Ref Series No = 13 Found 2032 files, checking for dicoms Found 2030 dicom files in series. First Sorting Computing Slice Direction Vs: 0.051 -0.354 2.4743 Vs: 0.0203999 -0.141599 0.989714 Second Sorting Counting frames nframes = 35 nslices = 58 ndcmfiles = 2030 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=6600.00, TE=84.20, TI=0.00, flip angle=90.00 i_ras = (-0.999791, -0.00289925, -0.0202339) j_ras = (0, -0.989897, 0.141789) k_ras = (-0.0203999, 0.141599, 0.989714) writing to /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz... mri_probedicom --i /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dcminfo.dat cp /home/ajfurst/Data/WRIISC/scripts/30+5gradtable.txt /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvecs cp /home/ajfurst/Data/WRIISC/scripts/bvalfile_1sess.txt /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvals flip4fsl /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2.19727 fslswapdim /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz x -y z /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz INFO: found /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.mghdti.bvecs /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.mghdti.bvals /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvals eddy_correct /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.nii.gz 0 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0001 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0002 processing
[Freesurfer] distortion metric question
Hi All, Is there a way to examine the distortion metric of the freesurfer surface normalization ? Please let me know. Thanks Ri ___ 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] tksurfer display
Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn ___ 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] tksurfer display
Can you describe the hardware / video card you are using? - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Thu, Sep 22, 2011 at 12:12, Peter Glynn pgl...@bu.edu wrote: Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn ___ 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] Stupid FsFastTutorialV5.1/TutorialData question
Yes, you can do that (that is what I was trying to communicate in the tutorial:). You can also just set your SUBJECTS_DIR to point to the FSFAST tutorial subjects. doug Carl Anderson wrote: Dear Free Surfer, At the bottom of http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/TutorialData it is stated: You will also need to link the FreeSurfer http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer anatomical subjeccts (data in fsfast-tutorial.subjects) into your $SUBJECTS_DIR My stupid question: Could this be accomplished by creating subdirectories or links in $SUBJECTS_DIR? Thanks, -- •~~•~~•~~•~~•~~•~~•~~• 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.
Re: [Freesurfer] Manual editing after recon-all
Hi Bruce, Yes, this is patient population. I ran the following command after adding control points along the white surface: recon-all -autorecon2 -autorecon3 -subjid subj Thanks for the offer to try out reconstruction in the data. I have uploaded the dataset and allowed access by you and Khoa. Kindly let me know if I should include others. Thanks and regards, Sindhuja Hi Sindhuja is this a patient population? It looks to me like there are lesions in the gray matter which will definitely mess up the pial surface deformation. We can try some things if you want to upload the data cheers Bruce On Sat, 17 Sep 2011, Sindhuja Tirumalai Govindarajan wrote: Hi Bruce and Khoa, I've attached the snapshots after adding control points and using autorecon2. So it looks like the control points extended the pial surface by a bit, but there is still some gray matter is left out. The same was observed in some other dataset as well. What command did you run? Do you want to upload the dataset? On Sep 16, 2011, at 10:52 PM, Sindhuja Tirumalai Govindarajan sindh...@nmr.mgh.harvard.edu wrote: Hi Khoa and Bruce, I added control points along the white surface - it did not help much in extending the pial surface. Looks like there might be some kind of gray matter pathology there as well On Sep 16, 2011, at 3:07 PM, Khoa Nguyen k...@nmr.mgh.harvard.edu wrote: Hi, How is the intensity of the wm between the putamen and the white surface? If it's lower than 110, you can place a string of control points along the inside border of the white surface. That might help extend the pial surf to include all the gm. -Khoa On Fri, 16 Sep 2011, Sindhuja Tirumalai Govindarajan wrote: Hi all, I ran into an issue similar to the manual editing problem discussed yesterday and earlier today. The pial surface seems to cut into the gray matter regions. However, there seems to be no wm problem in the neighborhood. Are there any tools to fix this? I have attached snapshots for your reference. Any advice on how to include the gray matter would be helpful! Thanks, Sindhuja ___ 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] Fwd: FW: flipped orientation in tksurfer and tkmedit
Ilana Hairston wrote: Hi Doug, The the subject data is uploaded, however it seems that we have figured out the issue - so you may not need to look at it. Below is what we think the problem and its solution are. Let me know if it makes sense. the reconstruction scripts at our campus imaging facility have two flaws: [1] there's is no orientation information in header of either Analyze or NIFTII outputs; [2] the Analyze format is non-standard (RAS instead of LAS). As a result the first mri_convert step which converts our file to .mgz format assumes that the orientation is neurological resulting in a flip of left to right (albeit with an error message saying that it did not have that info). this flipping can only be seen when comparing images in tkmedit and SPM, which should have been inveresed, but were not. We think that in order to avoid this in future we should add a --in-orientation ras flag to mri_convert. Is that correct? That might work. The orientation string is actually more specific than just RAS. You data might in an RAS cooridnate system, but this means that the orientation string could be RAS, or it could be SAR, or ARS, or ARS, etc. See what I mean? If it shows up correctly in tkmedit, then you're got it right (assuming that you are sure that it is really in an RAS coordinate system). The other question is - now that we have processed some 50 subjects, is there a way of flipping the results so that we wont have to start from scratch (this is a longitudinal study and participants will be scanned again).? You can try using xhemireg --s reversedsubject --o newsubjectname --all-vol --noreg This script was never intended for this purpose, so I don't know whether it will work fully or not. It should at least reverse all the volumes after which you can run recon-all on it. It should keep any edits you have made, but the control points won't be copied (and would be wrong in the reversed subject). doug Thanks Ilana -- ** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property -- 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] Cortical Thickness in significant clusters
Hi Antonella, I'm not sure what the problem is. You found clusters that are significant but the raw values are not different? doug Antonella Kis wrote: Dear Doug, I know as you told me in past that the average value for the cortical thickness in significant clusters is given in the cache.th20.neg.y.ocn.dat file under lh-Avg-thickness-age-Cor file. 1).Is there another way to get the cortical thickness for the significant clusters, other than read them from the cache.th20.neg.y.ocn.dat file? Analyzing my results for patients in lh with abnormal left side (due epilepsy) I realize that my cortical thickness values in this patients are not different (small difference) from the controls values. 2)Maybe I did a mistake while setting the FSGD (Y.fsgd) or what other mistake I could do because the cortical thickness should be different in this patients versus controls? I attached my FSGD matrix as well as my cortical thickness values in the significant clusters. Thank you very much for your time and help. AK -- 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] Contrast Vector while eliminating age and gender
Have you looked at the FSGD examples on the wiki? Do a search for FSGD. doug Antonella Kis wrote: Dear All, What should be my contrast vector if I want to do a direct comparison between groups (patients vs. controls) after eliminating gender and age? Should this be [1 -1]? Should I change my FSGD in order to be able to compare between patients and controls accounting for age (I want to make sure that the age does not confound my results). Please see attached my FSGD file. Also, my question is how the clusters are created: the clusters formation is due to a similar value within cortical thickness(cortical thickness with similar values from patients and controls are grouped together in a cluster (e.g. cluster no.1) while other cortical thickness values are forming different clusters) or the clusters are formed based on age -age grouping (each subject belong to an age cluster)? Thank you, AK -- 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] distortion metric question
There's not a way to get the distortion component of the cost function, but the jacobian will tell you how much the area had to expand/contract to fit the target surface. doug Ritobrato Datta wrote: Hi All, Is there a way to examine the distortion metric of the freesurfer surface normalization ? Please let me know. Thanks Ri ___ 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] tksurfer display
I am using an nVidia Quadro NVS 295 video card with an Intel(R) Xeon(R) CPU E5530 @2.4 GHz On Thu, Sep 22, 2011 at 11:37 AM, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: Interesting. I've had this problem trying to view the data on my dual boot Windows PC by remotely login with SSH to the linux server while running Xming or Hummingbird Exceed on the PC side. (Output image attached). Could it be some 3D rendering issue? I have no problem viewing the surfaces from my local ubuntu linux running freesurfer. tkmedit displays volumes properly. Jim -- *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Glynn *Sent:* Thu 9/22/2011 10:12 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] tksurfer display Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ___ 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] tksurfer display
attached find the output image. It looks very similar to Jim's, just rotated 180 degrees. On Thu, Sep 22, 2011 at 11:37 AM, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: Interesting. I've had this problem trying to view the data on my dual boot Windows PC by remotely login with SSH to the linux server while running Xming or Hummingbird Exceed on the PC side. (Output image attached). Could it be some 3D rendering issue? I have no problem viewing the surfaces from my local ubuntu linux running freesurfer. tkmedit displays volumes properly. Jim -- *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Glynn *Sent:* Thu 9/22/2011 10:12 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] tksurfer display Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. attachment: Screenshot-bert.png___ 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] trac-all results
Hi Ping, Did you try adjusting the threshold for left cst tract? In freeview you can find the tract labels in the left corner, if you click on the left cst tract and use the threshold button below to decrease the threshold. Please let us know if that improves the visualization. Cheers, Priti Hello, The segmented left CST tracts of one of our 3T data was not satisfactory, which has only few voxels with 1000 gray values (see attached snapshot pictures for trac-all and cst_prob). The manually tracking using deterministic tractography seems OK (see cst_stremline). Any suggestions on which step may go wrong in trac-all? Thank you, Ping ___ 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] tksurfer display
We worked on this months ago and decided to locally install linux on our dual boot PCs rather than remotely accessing data generated on our linux server via Windows (via SHH with Exceed or Xming). Perhaps there is an OpenGL issue? JIm From: Peter Glynn [mailto:pgl...@bu.edu] Sent: Thu 9/22/2011 11:21 AM To: Alexopoulos, Dimitrios Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer display attached find the output image. It looks very similar to Jim's, just rotated 180 degrees. On Thu, Sep 22, 2011 at 11:37 AM, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: Interesting. I've had this problem trying to view the data on my dual boot Windows PC by remotely login with SSH to the linux server while running Xming or Hummingbird Exceed on the PC side. (Output image attached). Could it be some 3D rendering issue? I have no problem viewing the surfaces from my local ubuntu linux running freesurfer. tkmedit displays volumes properly. Jim From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Glynn Sent: Thu 9/22/2011 10:12 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] tksurfer display Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ___ 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] trac-all results
Hi Ping - It looks like the path initialization may have failed. The algorithm needs an initial guess for the path and iterates from there. This initial guess is chosen based on the tracts in the atlas and if your subject is not perfectly aligned with the atlas this initial guess might end up going off the white matter for example. Does the blue line in your snapshot look like it may not coincide well with you subject's CST, going off the white matter close to the end, etc? a.y On Thu, 22 Sep 2011, Ping-Hong Yeh wrote: Hello, The segmented left CST tracts of one of our 3T data was not satisfactory, which has only few voxels with 1000 gray values (see attached snapshot pictures for trac-all and cst_prob). The manually tracking using deterministic tractography seems OK (see cst_stremline). Any suggestions on which step may go wrong in trac-all? Thank you, Ping ___ 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] trac-all results
Hi Priti, Adjusting the threshold does not help. Indeed, the voxel number, only about 50 or so, is much less compared to right cst, which has couple thousands. In addition, the segmented image is a binary image, i.e. only intensity 0 and 1000, while other tracts have gray scale ranging from 0 to 100 or so. ping On Thu, Sep 22, 2011 at 12:33 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Ping, Did you try adjusting the threshold for left cst tract? In freeview you can find the tract labels in the left corner, if you click on the left cst tract and use the threshold button below to decrease the threshold. Please let us know if that improves the visualization. Cheers, Priti Hello, The segmented left CST tracts of one of our 3T data was not satisfactory, which has only few voxels with 1000 gray values (see attached snapshot pictures for trac-all and cst_prob). The manually tracking using deterministic tractography seems OK (see cst_stremline). Any suggestions on which step may go wrong in trac-all? Thank you, Ping ___ 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] tksurfer display
I found this site for the type of problem we are having with tksurfer http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems Jim From: Peter Glynn [mailto:pgl...@bu.edu] Sent: Thu 9/22/2011 11:21 AM To: Alexopoulos, Dimitrios Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer display attached find the output image. It looks very similar to Jim's, just rotated 180 degrees. On Thu, Sep 22, 2011 at 11:37 AM, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: Interesting. I've had this problem trying to view the data on my dual boot Windows PC by remotely login with SSH to the linux server while running Xming or Hummingbird Exceed on the PC side. (Output image attached). Could it be some 3D rendering issue? I have no problem viewing the surfaces from my local ubuntu linux running freesurfer. tkmedit displays volumes properly. Jim From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Glynn Sent: Thu 9/22/2011 10:12 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] tksurfer display Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ___ 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] Discrete and Continuous factors in QDEC
Hi Doug, One more question please: if I want to do a cortical thickness study between two groups (patients and controls) and I want to eliminate the age and gender what should be my Discrete and Continuous factors in QDEC? Thank you. AK ___ 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] Discrete and Continuous factors in QDEC
Age as a continuous factor Gender as a discrete factor doug Antonella Kis wrote: Hi Doug, One more question please: if I want to do a cortical thickness study between two groups (patients and controls) and I want to eliminate the age and gender what should be my Discrete and Continuous factors in QDEC? Thank you. AK -- 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] tksurfer display
I have added this answer to the FAQ: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Thu, Sep 22, 2011 at 14:33, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: I found this site for the type of problem we are having with tksurfer http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems Jim -- *From:* Peter Glynn [mailto:pgl...@bu.edu] *Sent:* Thu 9/22/2011 11:21 AM *To:* Alexopoulos, Dimitrios *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] tksurfer display attached find the output image. It looks very similar to Jim's, just rotated 180 degrees. On Thu, Sep 22, 2011 at 11:37 AM, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: Interesting. I've had this problem trying to view the data on my dual boot Windows PC by remotely login with SSH to the linux server while running Xming or Hummingbird Exceed on the PC side. (Output image attached). Could it be some 3D rendering issue? I have no problem viewing the surfaces from my local ubuntu linux running freesurfer. tkmedit displays volumes properly. Jim -- *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Glynn *Sent:* Thu 9/22/2011 10:12 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] tksurfer display Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ___ 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] mri_watershed for inner_skull_surface question
Hi Bruce, Thanks for responding. We do have T2, but not PD. Of course the resolution of the T2 is much lower (5mm slices). -roddy -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, September 21, 2011 7:54 AM To: Roderick McColl; Matti Hamalainen Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed for inner_skull_surface question Matti Hamalainen (ccd) might have some thoughts. Do you have T2 or PD images? cheers Bruce On Tue, 20 Sep 2011, Roderick McColl wrote: Hi all, Trying to get mri_watershed to give me a good inner_skull_surface, which I want to combine with the pial surface to estimate sulcal CSF, as I don't see any other way. Unfortunately the data I have tested on all generate unreliable inner_skull surfaces. Can anyone provide a tip for optimizing the result? Thanks -roddy __ __ ___ UT Southwestern Medical Center The future of medicine, today. 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] Contrast Vector while eliminating age and gender
If you want to eliminate age and gender, you have to include them in the model. In this case, they are called nuisance regressors. But this is just an arbitrary name. The model is constructed of regressors, some of which you care about and some you don't, but the GLM is run in the same way regardless. Where the difference comes is when you go to construct contrast vectors. If you want to treat some regressors as nuisance, then put a 0 in their column in the contrast vector. doug Antonella Kis wrote: Hi Doug, Yes, I looked online but in all the examples I found age was included in the study. The same thing for qdec all the examples I saw online are related to a study (a comparison between two groups) but considering age. I couldn't find any documentation for a study between two groups while eliminating age and gender. Please advise and sorry for all this questions. Regards, Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, September 22, 2011 12:03 PM *Subject:* Re: [Freesurfer] Contrast Vector while eliminating age and gender Have you looked at the FSGD examples on the wiki? Do a search for FSGD. doug Antonella Kis wrote: Dear All, What should be my contrast vector if I want to do a direct comparison between groups (patients vs. controls) after eliminating gender and age? Should this be [1 -1]? Should I change my FSGD in order to be able to compare between patients and controls accounting for age (I want to make sure that the age does not confound my results). Please see attached my FSGD file. Also, my question is how the clusters are created: the clusters formation is due to a similar value within cortical thickness(cortical thickness with similar values from patients and controls are grouped together in a cluster (e.g. cluster no.1) while other cortical thickness values are forming different clusters) or the clusters are formed based on age -age grouping (each subject belong to an age cluster)? Thank you, AK -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto: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 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. -- 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
[Freesurfer] Fwd: Fwd: FW: flipped orientation in tksurfer and tkmedit
Hi Doug, Sorry, that this is turning into a saga. The xhemireg command ran, but then recon-all failed (we used recon-all -all). Also it seems there are missing surfaces, we can't load wm and pial, the surf directory is empty. Although that maybe because the recon didn't run. Thanks i. -- Forwarded message -- From: Chelsea Cummiford chelsea.cummif...@gmail.com Date: Thu, Sep 22, 2011 at 4:35 PM Subject: Re: [Freesurfer] Fwd: FW: flipped orientation in tksurfer and tkmedit To: Ilana Hairston hairstons...@gmail.com [chelsea@hypnos ilanagroup]$ recon-all -all -subjid FlippedFS091205dc/ Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/FS51/subjects/ilanagroup Actual FREESURFER_HOME /usr/local/FS51 -rw-rw-r-- 1 chelsea ZL 16132 Sep 22 15:37 /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/scripts/recon-all.log Linux hypnos 2.6.18-238.el5 #1 SMP Thu Jan 13 15:51:15 EST 2011 x86_64 x86_64 x86_64 GNU/Linux # #@# MotionCor Thu Sep 22 16:35:06 EDT 2011 ERROR: no run data found in /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/mri. Make sure to have a volume called 001.mgz in /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux hypnos 2.6.18-238.el5 #1 SMP Thu Jan 13 15:51:15 EST 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s FlippedFS091205dc exited with ERRORS at Thu Sep 22 16:35:06 EDT 2011 For more details, see the log file /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On Thu, Sep 22, 2011 at 4:32 PM, Ilana Hairston hairstons...@gmail.comwrote: can you paste in the errors? i'll forward them to the freesurfer list On Thu, Sep 22, 2011 at 3:43 PM, Chelsea Cummiford chelsea.cummif...@gmail.com wrote: ok, so the xhemireg command ran fine, but I can't run recon-all -all - it exits with errors. says that there is no 001.mgz file. I can pull it up in tkmedit (albeit, none of the control points or grey/white matter lines show up). the brain is flipped compared to the original though. On Thu, Sep 22, 2011 at 3:30 PM, Chelsea Cummiford chelsea.cummif...@gmail.com wrote: oh, got it. i thought you meant check both commands... will do. On Thu, Sep 22, 2011 at 3:26 PM, Ilana Hairston hairstons...@gmail.comwrote: no this one, to invert the brains that are already processed xhemireg --s reversedsubject --o newsubjectname --all-vol --noreg On Thu, Sep 22, 2011 at 3:24 PM, Chelsea Cummiford chelsea.cummif...@gmail.com wrote: do you mean running the --in-orientation ras command and then running recon-all?? because we did that and it looks fine in tkmedit and tksurfer - right heng? this is what FS00wh is... On Thu, Sep 22, 2011 at 2:57 PM, Ilana Hairston hairstons...@gmail.com wrote: Seems like we need to be 100% sure that our analyze/nifti is RAS. Chelsea, could you check the second command, followed by recon-all (i assume recon-all all) ? thx i We think that in order to avoid this in future we should add a --in-orientation ras flag to mri_convert. Is that correct? That might work. The orientation string is actually more specific than just RAS. You data might in an RAS cooridnate system, but this means that the orientation string could be RAS, or it could be SAR, or ARS, or ARS, etc. See what I mean? If it shows up correctly in tkmedit, then you're got it right (assuming that you are sure that it is really in an RAS coordinate system). The other question is - now that we have processed some 50 subjects, is there a way of flipping the results so that we wont have to start from scratch (this is a longitudinal study and participants will be scanned again).? You can try using xhemireg --s reversedsubject --o newsubjectname --all-vol --noreg This script was never intended for this purpose, so I don't know whether it will work fully or not. It should at least reverse all the volumes after which you can run recon-all on it. It should keep any edits you have made, but the control points won't be copied (and would be wrong in the reversed subject). doug Thanks Ilana -- ** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs:
Re: [Freesurfer] Fwd: Fwd: FW: flipped orientation in tksurfer and tkmedit
I don't know what that is about. Can you try using this version: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg Ilana Hairston wrote: Hi Doug, Sorry, that this is turning into a saga. The xhemireg command ran, but then recon-all failed (we used recon-all -all). Also it seems there are missing surfaces, we can't load wm and pial, the surf directory is empty. Although that maybe because the recon didn't run. Thanks i. -- Forwarded message -- From: *Chelsea Cummiford* chelsea.cummif...@gmail.com mailto:chelsea.cummif...@gmail.com Date: Thu, Sep 22, 2011 at 4:35 PM Subject: Re: [Freesurfer] Fwd: FW: flipped orientation in tksurfer and tkmedit To: Ilana Hairston hairstons...@gmail.com mailto:hairstons...@gmail.com [chelsea@hypnos ilanagroup]$ recon-all -all -subjid FlippedFS091205dc/ Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/FS51/subjects/ilanagroup Actual FREESURFER_HOME /usr/local/FS51 -rw-rw-r-- 1 chelsea ZL 16132 Sep 22 15:37 /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/scripts/recon-all.log Linux hypnos 2.6.18-238.el5 #1 SMP Thu Jan 13 15:51:15 EST 2011 x86_64 x86_64 x86_64 GNU/Linux # #@# MotionCor Thu Sep 22 16:35:06 EDT 2011 ERROR: no run data found in /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/mri. Make sure to have a volume called 001.mgz in /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux hypnos 2.6.18-238.el5 #1 SMP Thu Jan 13 15:51:15 EST 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s FlippedFS091205dc exited with ERRORS at Thu Sep 22 16:35:06 EDT 2011 For more details, see the log file /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On Thu, Sep 22, 2011 at 4:32 PM, Ilana Hairston hairstons...@gmail.com mailto:hairstons...@gmail.com wrote: can you paste in the errors? i'll forward them to the freesurfer list On Thu, Sep 22, 2011 at 3:43 PM, Chelsea Cummiford chelsea.cummif...@gmail.com mailto:chelsea.cummif...@gmail.com wrote: ok, so the xhemireg command ran fine, but I can't run recon-all -all - it exits with errors. says that there is no 001.mgz file. I can pull it up in tkmedit (albeit, none of the control points or grey/white matter lines show up). the brain is flipped compared to the original though. On Thu, Sep 22, 2011 at 3:30 PM, Chelsea Cummiford chelsea.cummif...@gmail.com mailto:chelsea.cummif...@gmail.com wrote: oh, got it. i thought you meant check both commands... will do. On Thu, Sep 22, 2011 at 3:26 PM, Ilana Hairston hairstons...@gmail.com mailto:hairstons...@gmail.com wrote: no this one, to invert the brains that are already processed xhemireg --s reversedsubject --o newsubjectname --all-vol --noreg On Thu, Sep 22, 2011 at 3:24 PM, Chelsea Cummiford chelsea.cummif...@gmail.com mailto:chelsea.cummif...@gmail.com wrote: do you mean running the --in-orientation ras command and then running recon-all?? because we did that and it looks fine in tkmedit and tksurfer - right heng? this is what FS00wh is... On Thu, Sep 22, 2011 at 2:57 PM, Ilana Hairston hairstons...@gmail.com mailto:hairstons...@gmail.com wrote: Seems like we need to be 100% sure that our analyze/nifti is RAS. Chelsea, could you check the second command, followed by recon-all (i assume recon-all all) ? thx i We think that in order to avoid this in future we should add a --in-orientation ras flag to mri_convert. Is that correct? That might work. The orientation string is actually more specific than just RAS. You data might in an RAS cooridnate system, but this means that the orientation string could be RAS, or it could be SAR, or ARS, or ARS, etc. See what I mean? If it shows up correctly
[Freesurfer] structure volume dti_recon vs recon_all
Hi, After running dti_recon and recon_all, I noticed that they produce different volumes of various structures for the same brain. Just trying to understand why that is? best, AJ ___ 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.
