Re: [Freesurfer] after PialEdit_tktools
Dear all, Can I just type recon-all -autorecon-pial -autorecon3 -s subjects after editing the pial by PialEdit_tktools? All the best 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com 发件人：Rujing Zha zh...@mail.ustc.edu.cn 发送时间：2013-12-10 12:03 主题：[Freesurfer] after PialEdit_tktools 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Dear all, I run recon-all -autorecon-pial -s subjects after editing the pial by PialEdit_tktools. However I only find -autorecon2-pial option in recon-all manual. So I donot know whether I should run the recon-all -s subjects -autorecon3 to complete all the 31 stages? Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ 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] after PialEdit_tktools
Hi Rujing, yes, you should run -autorecon2-pial -autorecon3 cheers Bruce On Tue, 10 Dec 2013, Rujing Zha wrote: Dear all, I run recon-all -autorecon-pial -s subjects after editing the pial by PialEdit_tktools. However I only find -autorecon2-pial option in recon-all manual. So I donot know whether I should run the recon-all -s subjects -autorecon3 to complete all the 31 stages? Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ 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] Occipital cortex segmentation
Hi Megha looking at your images it's not clear to me where the gray/white boundary is. Do you think it should be further out? One thing you can try is (if the occipital white matter intensity in brain.mgz is 110) putting some control points in the interior of the white matter. Or as Matt suggests, higher resolution can help, but that may not be an option cheers Bruce On Tue, 10 Dec 2013, Megha K. wrote: Dear Sir/Madam, I am using freesurfer for 3T MRI analysis of visual cortical thickness in elderly patients with ophthalmic disease. We are having a bit of trouble with the accuracy of cortical segmentation in the visual cortex (namely the pericalcarine region) as the cortex is quite thin in our patients (compared to controls). You can see in the attached image that whilst there is smooth cortical segmentation in the peri-calcarine region, the cortex is not visible to the naked eye. If you have any ideas on improving accuracy, I would be very grateful. Thanks Megha ___ 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] after PialEdit_tktools
yes, with -s subjects replaced with -s subject id On Tue, 10 Dec 2013, Rujing Zha wrote: Dear all, Can I just type recon-all -autorecon-pial -autorecon3 -s subjects after editing the pial by PialEdit_tktools? All the best 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com 发件人：Rujing Zha zh...@mail.ustc.edu.cn 发送时间：2013-12-10 12:03 主题：[Freesurfer] after PialEdit_tktools 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Dear all, I run recon-all -autorecon-pial -s subjects after editing the pial by PialEdit_tktools. However I only find -autorecon2-pial option in recon-all manual. So I donot know whether I should run the recon-all -s subjects -autorecon3 to complete all the 31 stages? Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ 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] after PialEdit_tktools
Dear Bruce, In PialEdit_tktools http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_tktools, it say this: recon-all -autorecon-pial -subjid pial_edits_before .So I didnot know whether the -autorecon-pial option -autorecon2-pial option I can run. Would you please tell me which one I should use? Thanks. All the best. 2013-12-10 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-10 21:17 主题：Re: [Freesurfer] after PialEdit_tktools 收件人：Rujing Zhazh...@mail.ustc.edu.cn 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, yes, you should run -autorecon2-pial -autorecon3 cheers Bruce On Tue, 10 Dec 2013, Rujing Zha wrote: Dear all, I run recon-all -autorecon-pial -s subjects after editing the pial by PialEdit_tktools. However I only find -autorecon2-pial option in recon-all manual. So I donot know whether I should run the recon-all -s subjects -autorecon3 to complete all the 31 stages? Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ 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] after PialEdit_tktools
sorry, looking at the script, I think: recon-all -autorecon-pial -s subject name should be all you need, but perhaps someone else can confirm. Bruce On Tue, 10 Dec 2013, Rujing Zha wrote: Dear Bruce, In PialEdit_tktools http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_tktools, it say this: recon-all -autorecon-pial -subjid pial_edits_before .So I didnot know whether the -autorecon-pial option -autorecon2-pial option I can run. Would you please tell me which one I should use? Thanks. All the best. 2013-12-10 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-10 21:17 主题：Re: [Freesurfer] after PialEdit_tktools 收件人：Rujing Zhazh...@mail.ustc.edu.cn 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, yes, you should run -autorecon2-pial -autorecon3 cheers Bruce On Tue, 10 Dec 2013, Rujing Zha wrote: Dear all, I run recon-all -autorecon-pial -s subjects after editing the pial by PialEdit_tktools. However I only find -autorecon2-pial option in recon- all manual. So I donot know whether I should run the recon-all -s subjects -autorecon3 to complete all the 31 stages? Thanks. All the best. 2013-12-10 _ ___ Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ 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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly 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] after PialEdit_tktools
Dear Bruce, Thanks. I see. All the best. 2013-12-10 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-10 21:29 主题：Re: [Freesurfer] after PialEdit_tktools 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu sorry, looking at the script, I think: recon-all -autorecon-pial -s subject name should be all you need, but perhaps someone else can confirm. Bruce On Tue, 10 Dec 2013, Rujing Zha wrote: Dear Bruce, In PialEdit_tktools http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_tktools, it say this: recon-all -autorecon-pial -subjid pial_edits_before .So I didnot know whether the -autorecon-pial option -autorecon2-pial option I can run. Would you please tell me which one I should use? Thanks. All the best. 2013-12-10 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-10 21:17 主题：Re: [Freesurfer] after PialEdit_tktools 收件人：Rujing Zhazh...@mail.ustc.edu.cn 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, yes, you should run -autorecon2-pial -autorecon3 cheers Bruce On Tue, 10 Dec 2013, Rujing Zha wrote: Dear all, I run recon-all -autorecon-pial -s subjects after editing the pial by PialEdit_tktools. However I only find -autorecon2-pial option in recon- all manual. So I donot know whether I should run the recon-all -s subjects -autorecon3 to complete all the 31 stages? Thanks. All the best. 2013-12-10 _ ___ Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ 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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly 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.
[Freesurfer] part of GM missing
Dear all, In tkmedit brainmask.mgz -surfs, there are a bit of GM part missing. I want to know how to paint the voxels to lable it as GM. And then run recon-all in a specific style to reconstruct the surfs. Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ 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 values of significant clusters
your interpretation is correct. Here's the matlab code
cd glmdir/yourcontrast
X = load('../Xg.dat');
C = load('C.dat');
y = load('cache.th20.abs.y.ocn.dat');
[beta rvar] = fast_glmfit(y,X);
[F pvalues] = fast_fratio(beta,X,rvar,C);
pvalues will be an array with the pvalue for each cluster
make sure that $FREESURFER_HOME/fsfast/toolbox in in your matlab path
doug
On 12/10/2013 01:50 AM, Sinead Kelly wrote:
Hi Doug,
thank you for your reply. It is unusual as I also get a significant
result in SPSS for a non-significant cluster in mri-glmfit. Just to
make sure I am doing things correctly - I am interpreting each column
in the xxx.y.ocn.dat file as a cluster in the xxx.sig.cluster.summary
file (in numerical order) so the first column in the y.ocn.dat file
corresponds to cluster 1 in the sig.cluster.summary file. I do have
matlab so if you have the code, that would be great.
Thanks so much again for your help,
Sinead
On 9 December 2013 19:52, Douglas Greve gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
That is the right file to use, and one would expect to see
significant results. Are you sure you are using exactly the same
model? If you have matlab, I can give you some code to do the
analysis using the exact model that mri_glmfit uses.
doug
On 12/9/13 10:43 PM, Sinead Kelly wrote:
Dear Freesurfer users,
I have just ran mri-glmfit on cortical thickness data and
corrected for multiple comparisons using Monte Carlo Simulation.
I have significant clusters (cwp .05), however, when I analyse
the average thickness measures from the xxx.y.ocn.dat file in
SPSS, there are no significant differences between my groups. I'm
not sure if I am using the correct approach to extract thickness
values for the significant clusters.
Thank you for your help,
Sinead
--
Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8
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Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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[Freesurfer] T1 FLASH parameters for cortical thickness analyses
Hi All, I have collected T1 3D FLASH on a subject and here are some details of the sequence, Manufacturer = SIEMENS StudyDescription = Neuro_3T^brain_3t SeriesDescription = Axial Global FLASH FA27 ManufacturersModelName = Verio ReferencedImageSequence = 1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835978\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835980\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835979 ScanningSequence = GR SequenceVariant = SP ScanOptions = SAT1 MRAcquisitionType = 3D SequenceName = *fl3d1 SliceThickness = 1 RepetitionTime = 20 EchoTime = 5 InversionTime = - NumberofAverages = 1 ImagingFrequency = 123.200338 ImagedNucleus = 1H EchoNumbers = 1 MagneticFieldStrength = 3 NumberofPhaseEncodingSteps = 192 EchoTrainLength = 1 PercentSampling = 100 PercentPhaseFieldofView = 75 PixelBandwidth = 179 DeviceSerialNumber = 40156 SoftwareVersions = syngo MR B17 ProtocolName = Axial Global FLASH FA27 TransmitCoilName = Body AcquisitionMatrix = 0\256\192\0 In-planePhaseEncodingDirection = ROW FlipAngle = 27 VariableFlipAngleFlag = N SAR = 0.19411263 My questions are the following - 1) Can I get reliable cortical thickness estimates using a T1 3D FLASH sequence at 3T Siemens TRIO ? 2) Which version of freesurfer is recommended ? 3) One reason, I collected T1 FLASH is I want to get whole brain volume and brain parenchymal fraction in Multiple sclerosis patients. But if freesurfer prefers MPRAGES over FLASH for cortical thickness, I am wondering how reliable are the standard MPRAGE sequences for calculation of whole brain volume and brain parenchymal fractions ? 4) I ran the recon on the FLASH using freesurfer 5.3 and it looks very decent but has anyone tested and optimized the parameters for the T1 FLASH sequence for cortical thickness estimations ? 5) If you can share your opinion and experiences in this topic and maybe point me to some references using flash and freesurfer for cortical thickness, that will be very helpful. Best 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.
Re: [Freesurfer] xhemi correct for multiple comparisons
Hi again, I've looked into mri_glmfit-sim --help to figure out which files I could overlay in tkurfer after correcting for multiple comparisons using the instructions for xhemi on the freesurfer wiki. However, I do not see any of these files (csd.base...) in the glmdir/osgm folder. I only see ones that begin with cache. Are these the files I should be overlaying? Or should I be using different commands for my analyses? here is the command line I used: mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \ --cwpvalthresh .5 --cache 2 abs Prior to mri_glmfit, I conducted the create a stack of subjects using paired-diff-norm in place of paired-diff Ultimately, I want to look at hemisphere asymmetries (preferably in terms of laterality indices) in two different groups separately. I would also like to see if laterality indices differ between groups. Is this possible? Thanks! Krista On Mon, Dec 9, 2013 at 4:00 PM, krista kelly krista.kell...@gmail.comwrote: Great Thanks! On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 12/09/2013 11:53 AM, krista kelly wrote: Thanks Doug! I'll try that instead. Also, do you or anyone else happen to have the answers to my other questions (reposted below): 1) When viewing the results in tksurfer, which color represents left hemisphere is larger and which represents right hemisphere is larger? If you are just doing a simple interhemispheric difference, then yellow/red will be leftright and blue leftright 2) I have no idea how to view the results in tksurfer AFTER performing the step of correcting for multiple comparisons. Any suggestions? If you run mri_glmfit-sim with --help you will see a list of output files with descriptions for each. Choose the one you want and run tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc -overlay csdbase.sig.cluster.mgh ) doug Thanks! Krista On Mon, Dec 9, 2013 at 11:09 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Run mris_preproc with --paired-diff-norm which will then compute LI = (L-R)/(.5*(L+R)) Note that some people use LI = (L-R)/(L+R) If that is what you want, then divide the mris_preproc result by 2 doug On 12/08/2013 08:45 PM, krista kelly wrote: Hello, I'm analysing interhemispheric differences using xhemi. I have followed the instructions on the webpage with no problems. I do have a few questions though. 1) When viewing the results in tksurfer, which color represents left hemisphere is larger and which represents right hemisphere is larger? 2) I have no idea how to view the results in tksurfer AFTER performing the step of correcting for multiple comparisons. Any suggestions? 3) I've noticed from the archives that some people are performing laterality indices. How would I calculate laterality indices? Thanks! Krista ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 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 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:
[Freesurfer] multiple frames error message for recon-all
Hi, I'm trying to do recon-all for a file, and it gave me this multiple frame error message: #@# MotionCor Mon Nov 25 13:11:40 EST 2013 Found 1 runs /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/orig/001.mgz has 4 frames If this is a multi-frame MEMPRAGE image, use mri_concat --rms to combine echo frames. Linux compute-0-73 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BHI_BJU-345_pre_lazar exited with ERRORS at Mon Nov 25 13:11:47 EST 2013 For more details, see the log file /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting May I ask what should I do to solve this problem? There are actually two files which give me the same error message: BHI_BJU-345_pre_lazar (pbsjob_30) and BHI_JJA-329_pre_lazar (pbsjob_33) Thanks, Noel --- Noel Yanki Chan, PhD Department of Psychiatry Neuroscience Laboratory of Sara Lazar, PhD Harvard Medical School Massachusetts General Hospital Building 120, 2nd avenue, Suite 103 Charlestown, MA 02129 Tel: 617-643-5078 (lab) 607-229-7096 (cell) ___ 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] T1 FLASH parameters for cortical thickness analyses
Hi Ri the sequence looks reasonable, although your TE of 5ms is somewhat long and will reduce CNR and SNR. Can you shorten it? I would think you should be able to. We looked at this for a while, and in the end the mprage outperformed FLASH in terms of cortical gray matter/cerebral white matter CNR/unit time. The FLASH scans were ok, but not as good as mprage. I think either is fine for ICV, although if you collect a lower fiip FLASH which will be PD weighted (e.g. a 5deg) then that will be an advantage for ICV. cheers Bruce On Tue, 10 Dec 2013, Ritobrato Datta wrote: Hi All, I have collected T1 3D FLASH on a subject and here are some details of the sequence, Manufacturer = SIEMENS StudyDescription = Neuro_3T^brain_3t SeriesDescription = Axial Global FLASH FA27 ManufacturersModelName = Verio ReferencedImageSequence = 1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835978\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835980\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835979 ScanningSequence = GR SequenceVariant = SP ScanOptions = SAT1 MRAcquisitionType = 3D SequenceName = *fl3d1 SliceThickness = 1 RepetitionTime = 20 EchoTime = 5 InversionTime = - NumberofAverages = 1 ImagingFrequency = 123.200338 ImagedNucleus = 1H EchoNumbers = 1 MagneticFieldStrength = 3 NumberofPhaseEncodingSteps = 192 EchoTrainLength = 1 PercentSampling = 100 PercentPhaseFieldofView = 75 PixelBandwidth = 179 DeviceSerialNumber = 40156 SoftwareVersions = syngo MR B17 ProtocolName = Axial Global FLASH FA27 TransmitCoilName = Body AcquisitionMatrix = 0\256\192\0 In-planePhaseEncodingDirection = ROW FlipAngle = 27 VariableFlipAngleFlag = N SAR = 0.19411263 My questions are the following - 1) Can I get reliable cortical thickness estimates using a T1 3D FLASH sequence at 3T Siemens TRIO ? 2) Which version of freesurfer is recommended ? 3) One reason, I collected T1 FLASH is I want to get whole brain volume and brain parenchymal fraction in Multiple sclerosis patients. But if freesurfer prefers MPRAGES over FLASH for cortical thickness, I am wondering how reliable are the standard MPRAGE sequences for calculation of whole brain volume and brain parenchymal fractions ? 4) I ran the recon on the FLASH using freesurfer 5.3 and it looks very decent but has anyone tested and optimized the parameters for the T1 FLASH sequence for cortical thickness estimations ? 5) If you can share your opinion and experiences in this topic and maybe point me to some references using flash and freesurfer for cortical thickness, that will be very helpful. Best Ri ___ 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] multiple frames error message for recon-all
Hi Noel what were the acquisitions? If they were multi-echo mprage than you will either have to generate the RMS or find the series that is the RMS (since it should have been generated automatically) cheers Bruce On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D. wrote: Hi, I'm trying to do recon-all for a file, and it gave me this multiple frame error message: #@# MotionCor Mon Nov 25 13:11:40 EST 2013 Found 1 runs /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/ orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/ orig/001.mgz has 4 frames If this is a multi-frame MEMPRAGE image, use mri_concat --rms to combine echo frames. Linux compute-0-73 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BHI_BJU-345_pre_lazar exited with ERRORS at Mon Nov 25 13:11:47 EST 2013 For more details, see the log file/autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/scri pts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting May I ask what should I do to solve this problem? There are actually two files which give me the same error message: BHI_BJU-345_pre_lazar (pbsjob_30) and BHI_JJA-329_pre_lazar (pbsjob_33) Thanks, Noel --- Noel Yanki Chan, PhD Department of Psychiatry Neuroscience Laboratory of Sara Lazar, PhD Harvard Medical School Massachusetts General Hospital Building 120, 2nd avenue, Suite 103 Charlestown, MA 02129 Tel: 617-643-5078 (lab) 607-229-7096 (cell) ___ 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] xhemi correct for multiple comparisons
Yes, use the cache files. When --cache is used, the csdbase=cache On 12/10/2013 12:20 PM, krista kelly wrote: Hi again, I've looked into mri_glmfit-sim --help to figure out which files I could overlay in tkurfer after correcting for multiple comparisons using the instructions for xhemi on the freesurfer wiki. However, I do not see any of these files (csd.base...) in the glmdir/osgm folder. I only see ones that begin with cache. Are these the files I should be overlaying? Or should I be using different commands for my analyses? here is the command line I used: mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \ --cwpvalthresh .5 --cache 2 abs Prior to mri_glmfit, I conducted the create a stack of subjects using paired-diff-norm in place of paired-diff Ultimately, I want to look at hemisphere asymmetries (preferably in terms of laterality indices) in two different groups separately. I would also like to see if laterality indices differ between groups. Is this possible? Thanks! Krista On Mon, Dec 9, 2013 at 4:00 PM, krista kelly krista.kell...@gmail.com mailto:krista.kell...@gmail.com wrote: Great Thanks! On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 12/09/2013 11:53 AM, krista kelly wrote: Thanks Doug! I'll try that instead. Also, do you or anyone else happen to have the answers to my other questions (reposted below): 1) When viewing the results in tksurfer, which color represents left hemisphere is larger and which represents right hemisphere is larger? If you are just doing a simple interhemispheric difference, then yellow/red will be leftright and blue leftright 2) I have no idea how to view the results in tksurfer AFTER performing the step of correcting for multiple comparisons. Any suggestions? If you run mri_glmfit-sim with --help you will see a list of output files with descriptions for each. Choose the one you want and run tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc -overlay csdbase.sig.cluster.mgh ) doug Thanks! Krista On Mon, Dec 9, 2013 at 11:09 AM, Douglas N 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: Run mris_preproc with --paired-diff-norm which will then compute LI = (L-R)/(.5*(L+R)) Note that some people use LI = (L-R)/(L+R) If that is what you want, then divide the mris_preproc result by 2 doug On 12/08/2013 08:45 PM, krista kelly wrote: Hello, I'm analysing interhemispheric differences using xhemi. I have followed the instructions on the webpage with no problems. I do have a few questions though. 1) When viewing the results in tksurfer, which color represents left hemisphere is larger and which represents right hemisphere is larger? 2) I have no idea how to view the results in tksurfer AFTER performing the step of correcting for multiple comparisons. Any suggestions? 3) I've noticed from the archives that some people are performing laterality indices. How would I calculate laterality indices? Thanks! Krista ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Re: [Freesurfer] qdec analysis with 2 covariates
hmmm, it should be there. What version of FS are you using? On 12/10/2013 12:57 PM, Jon Wieser wrote: i was getting the values for the command terminal, when I press the find clusters and GOTo Max button on the qdec GUI. there is no file named cache.th20.abs.y.dat or something similar. i did a find command to list all the *abs*.dat files in the directory qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat these files contain: # CSD PDF/CDF # simtype null-z # anattype surface fsaverage lh # FixGroupSubjectArea 1 # merged 0 # contrastNA # seed1271277527 # thresh 1.30 # threshsign 0.00 # searchspace 74612.965197 # nullfwhm15.00 # varfwhm -1.00 # nrepetitions 1 # NOTE: nreps and nrepetitions are both valid for volume data. # NOTE: nreps is invalid (-1) for surface data to assure. # NOTE: backwards INcompatibility. # $Id: volcluster.c,v 1.50.2.1 2011/03/28 15:32:36 greve Exp $ # nreps -1 # FixSurfClusterArea 1 # $Id: surfcluster.c,v 1.26.2.2 2011/11/10 16:01:11 greve Exp $ # nbins 100 # BinNo MaxClustBin MaxClustPDF MaxClustCDF GRFCDFMaxSigBin MaxSigPDF MaxSigCDF 0 204.826004 0.000500 0.999500 0.998289 2.456050 0.000500 0.999500 1 220.348267 0.001800 0.997700 0.996805 2.811329 0.008100 0.991400 2 235.870529 0.004300 0.993400 0.994388 3.166609 0.022200 0.969200 3 251.392792 0.007100 0.986300 0.990673 3.521888 0.030300 0.938900 4 266.915039 0.015600 0.970700 0.985251 3.877167 0.028900 0.91 5 282.437317 0.017500 0.953200 0.977702 4.232447 0.022600 0.887400 6 297.959595 0.021400 0.931800 0.967628 4.587726 0.015200 0.872200 7 313.481842 0.033600 0.898200 0.954689 4.943005 0.012300 0.859900 8 329.004089 0.036100 0.862100 0.938634 5.298285 0.009800 0.850100 9 344.526367 0.038000 0.824100 0.919325 5.653563 0.007300 0.842800 10 360.048645 0.042500 0.781600 0.896747 6.008843 0.009200 0.833600 11 375.570892 0.05 0.731600 0.871009 6.364122 0.006900 0.826700 12 391.093140 0.043400 0.688200 0.842332 6.719401 0.007100 0.819600 13 406.615417 0.047300 0.640900 0.811034 7.074681 0.005500 0.814100 14 422.137695 0.050700 0.590200 0.777508 7.429960 0.005500 0.808600 15 437.659943 0.047400 0.542800 0.742195 7.785239 0.005200 0.803400 16 453.182190 0.044100 0.498700 0.705560 8.140518 0.004900 0.798500 17 468.704468 0.042700 0.456000 0.668070 8.495798 0.005100 0.793400 18 484.226746 0.040600 0.415400 0.630176 8.851077 0.006100 0.787300 19 499.748962 0.034900 0.380500 0.592300 9.206356 0.004800 0.782500 20 515.271240 0.032200 0.348300 0.554820 9.561636 0.003600 0.778900 21 530.793518 0.031400 0.316900 0.518067 9.916915 0.003400 0.775500 22 546.315796 0.032400 0.284500 0.482320 10.272194 0.004000 0.771500 23 561.838013 0.023800 0.260700 0.447809 10.627474 0.004800 0.766700 24 577.360291 0.026100 0.234600 0.414711 10.982753 0.004500 0.762200 25 592.882568 0.022700 0.211900 0.383160 11.338033 0.003300 0.758900 26 608.404846 0.017500 0.194400 0.353244 11.693312 0.003100 0.755800 27 623.927063 0.018200 0.176200 0.325018 12.048591 0.003700 0.752100 28 639.449341 0.017400 0.158800 0.298504 12.403871 0.003800 0.748300 29 654.971619 0.014900 0.143900 0.273697 12.759150 0.004400 0.743900 30 670.493896 0.014200 0.129700 0.250569 13.114429 0.003700 0.740200 31 686.016113 0.014300 0.115400 0.229078 13.469708 0.002800 0.737400 32 701.538391 0.013100 0.102300 0.209165 13.824987 0.003800 0.733600 33 717.060669 0.011700 0.090600 0.190763 14.180266 0.003700 0.729900 34 732.582947 0.008500 0.082100 0.173798 14.535546 0.002900 0.727000 35 748.105164 0.008400 0.073700 0.158191 14.890825 0.003200 0.723800 36
Re: [Freesurfer] Problems dipslaying annotations in freeview
I've seen this happen after making manual edits and then not finishing a re-run of recon-all. Chris On 12/10/2013 02:00 PM, Laura Taylor wrote: Hi, I'm trying to load lh.aparc.a2009s.annot onto the lh pial surface of a subject. When I use the freeview gui and select lh.aparc.a2009s.annot under the annotations menu a strange multicolored surface is loaded. It looks like something that has been tie-dyed and not like the examples of parcellation that are shown on some of the freesurfer pages. I have attached a screenshot of the output that I get. Any help would be appreciated. Thank you, Laura ___ 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] Problems dipslaying annotations in freeview
Yep, looks like your annot is out of sync with the surfaces On 12/10/2013 01:51 PM, Chris Watson wrote: I've seen this happen after making manual edits and then not finishing a re-run of recon-all. Chris On 12/10/2013 02:00 PM, Laura Taylor wrote: Hi, I'm trying to load lh.aparc.a2009s.annot onto the lh pial surface of a subject. When I use the freeview gui and select lh.aparc.a2009s.annot under the annotations menu a strange multicolored surface is loaded. It looks like something that has been tie-dyed and not like the examples of parcellation that are shown on some of the freesurfer pages. I have attached a screenshot of the output that I get. Any help would be appreciated. Thank you, Laura ___ 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 -- 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
[Freesurfer] optseq enforcing consecutive trials
Hi all, I posed a question back in November but got no replies, so I'll try to restate it briefly: Is there a means of enforcing at least one set of consecutive trials for a condition in an optseq schedule (or even consecutive trials with an intervening NULL event)? I am trying to produce a schedule for a 1-back task, and consecutive events for a given condition will only appear by chance. Getting at least one set of consecutive trials for each of 8 conditions has proven exceedingly difficult. Thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] qdec analysis with 2 covariates
Is there a cache.mri_glmfit-sim.log in the output folder? Can you send it to me? Also, please remember to post to the list. thanks! doug On 12/10/2013 02:30 PM, Jon Wieser wrote: FS version 5.3 - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:05:26 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates hmmm, it should be there. What version of FS are you using? On 12/10/2013 12:57 PM, Jon Wieser wrote: i was getting the values for the command terminal, when I press the find clusters and GOTo Max button on the qdec GUI. there is no file named cache.th20.abs.y.dat or something similar. i did a find command to list all the *abs*.dat files in the directory qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat these files contain: # CSD PDF/CDF # simtype null-z # anattype surface fsaverage lh # FixGroupSubjectArea 1 # merged 0 # contrastNA # seed1271277527 # thresh 1.30 # threshsign 0.00 # searchspace 74612.965197 # nullfwhm15.00 # varfwhm -1.00 # nrepetitions 1 # NOTE: nreps and nrepetitions are both valid for volume data. # NOTE: nreps is invalid (-1) for surface data to assure. # NOTE: backwards INcompatibility. # $Id: volcluster.c,v 1.50.2.1 2011/03/28 15:32:36 greve Exp $ # nreps -1 # FixSurfClusterArea 1 # $Id: surfcluster.c,v 1.26.2.2 2011/11/10 16:01:11 greve Exp $ # nbins 100 # BinNo MaxClustBin MaxClustPDF MaxClustCDF GRFCDFMaxSigBin MaxSigPDF MaxSigCDF 0 204.826004 0.000500 0.999500 0.998289 2.456050 0.000500 0.999500 1 220.348267 0.001800 0.997700 0.996805 2.811329 0.008100 0.991400 2 235.870529 0.004300 0.993400 0.994388 3.166609 0.022200 0.969200 3 251.392792 0.007100 0.986300 0.990673 3.521888 0.030300 0.938900 4 266.915039 0.015600 0.970700 0.985251 3.877167 0.028900 0.91 5 282.437317 0.017500 0.953200 0.977702 4.232447 0.022600 0.887400 6 297.959595 0.021400 0.931800 0.967628 4.587726 0.015200 0.872200 7 313.481842 0.033600 0.898200 0.954689 4.943005 0.012300 0.859900 8 329.004089 0.036100 0.862100 0.938634 5.298285 0.009800 0.850100 9 344.526367 0.038000 0.824100 0.919325 5.653563 0.007300 0.842800 10 360.048645 0.042500 0.781600 0.896747 6.008843 0.009200 0.833600 11 375.570892 0.05 0.731600 0.871009 6.364122 0.006900 0.826700 12 391.093140 0.043400 0.688200 0.842332 6.719401 0.007100 0.819600 13 406.615417 0.047300 0.640900 0.811034 7.074681 0.005500 0.814100 14 422.137695 0.050700 0.590200 0.777508 7.429960 0.005500 0.808600 15 437.659943 0.047400 0.542800 0.742195 7.785239 0.005200 0.803400 16 453.182190 0.044100 0.498700 0.705560 8.140518 0.004900 0.798500 17 468.704468 0.042700 0.456000 0.668070 8.495798 0.005100 0.793400 18 484.226746 0.040600 0.415400 0.630176 8.851077 0.006100 0.787300 19 499.748962 0.034900 0.380500 0.592300 9.206356 0.004800 0.782500 20 515.271240 0.032200 0.348300 0.554820 9.561636 0.003600 0.778900 21 530.793518 0.031400 0.316900 0.518067 9.916915 0.003400 0.775500 22 546.315796 0.032400 0.284500 0.482320 10.272194 0.004000 0.771500 23 561.838013 0.023800 0.260700 0.447809 10.627474 0.004800 0.766700 24 577.360291 0.026100 0.234600 0.414711 10.982753 0.004500 0.762200 25 592.882568 0.022700 0.211900 0.383160 11.338033 0.003300 0.758900 26 608.404846 0.017500 0.194400 0.353244 11.693312 0.003100 0.755800 27 623.927063 0.018200 0.176200 0.325018 12.048591 0.003700 0.752100 28 639.449341 0.017400 0.158800 0.298504 12.403871 0.003800 0.748300 29 654.971619 0.014900 0.143900 0.273697 12.759150 0.004400 0.743900 30 670.493896 0.014200 0.129700 0.250569 13.114429 0.003700 0.740200
Re: [Freesurfer] optseq enforcing consecutive trials
No, sorry. You might be able to treat two consecutive trials as a single trial, but then you won't get jitter between them. doug On 12/10/2013 02:38 PM, Chris McNorgan wrote: Hi all, I posed a question back in November but got no replies, so I'll try to restate it briefly: Is there a means of enforcing at least one set of consecutive trials for a condition in an optseq schedule (or even consecutive trials with an intervening NULL event)? I am trying to produce a schedule for a 1-back task, and consecutive events for a given condition will only appear by chance. Getting at least one set of consecutive trials for each of 8 conditions has proven exceedingly difficult. Thanks, Chris ___ 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.
Re: [Freesurfer] Problems dipslaying annotations in freeview
Hi, yes thank you both. That is exactly what the problem was. Laura On Tue, Dec 10, 2013 at 11:12 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Yep, looks like your annot is out of sync with the surfaces On 12/10/2013 01:51 PM, Chris Watson wrote: I've seen this happen after making manual edits and then not finishing a re-run of recon-all. Chris On 12/10/2013 02:00 PM, Laura Taylor wrote: Hi, I'm trying to load lh.aparc.a2009s.annot onto the lh pial surface of a subject. When I use the freeview gui and select lh.aparc.a2009s.annot under the annotations menu a strange multicolored surface is loaded. It looks like something that has been tie-dyed and not like the examples of parcellation that are shown on some of the freesurfer pages. I have attached a screenshot of the output that I get. Any help would be appreciated. Thank you, Laura ___ 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 -- 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 ___ 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] Do these bvec and bval files match?
Hello, I'm using TRACULA to analyze images obtained by a non-Siemens scanner, and I'm using dcm2niigui app to generate bvec and bval files from DICOMs. My question is whether or not the attached bvec and bval files match, because the 0 bval is the first entry while the 0,0,0 bvec is somewhere in the middle. If they don't, how should I generate the correct bval/bvec files from dicoms? Lots of thanks, Emad bval Description: Binary data bvec Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] multiple frames error message for recon-all
Thanks Bruce. I checked, it is multi-echo mprage, it's just when I unpack it, it didn't automatically generate the RMS. so can you walk me through when to do the mri-average-sqr? So I just type the command: unpacksdcmdir -src /cluster/archive/304/siemens/Skyra-45407-20130822-092226-174000 -targ . -scanonly unpacklogpre Then it gives me: Tue Dec 10 14:56:36 EST 2013 Log File is ./unpack.log INFO: Logfile is ./unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is ./dicomdir.sumfile INFO: status file is ./parse.status Scanning directory Tue Dec 10 14:56:36 EST 2013 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/304/siemens/Skyra-45407-20130822-092226-174000 --o ./dicomdir.sumfile --status ./parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Tue Dec 10 14:58:48 EST 2013 -- 1localizer ok 256 256 3 1 MR.1.3.12.2.1107.5.2.19.45407.2013082209234488137601798 2localizer ok 256 256 3 1 MR.1.3.12.2.1107.5.2.19.45407.2013082209234486217101797 3 AAHead_Scout ok 160 160 128 1 MR.1.3.12.2.1107.5.2.19.45407.2013082209242568708801865 4 AAHead_Scout ok 162 162 5 1 MR.1.3.12.2.1107.5.2.19.45407.2013082209243010322103111 5 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.19.45407.2013082209243010400603115 6 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.19.45407.2013082209243010456303118 7 MEMPRAGE_tfl_mgh_multiecho_1mm_iso ok 256 256 176 4 MR.1.3.12.2.1107.5.2.19.45407.2013082209321083146803580 8 fMRI_resting_state ok 72 72 47 124 MR.1.3.12.2.1107.5.2.19.45407.2013082209330867404606382 How do I create the RMS? Thanks, Noel --- Noel Yanki Chan, PhD Department of Psychiatry Neuroscience Laboratory of Sara Lazar, PhD Harvard Medical School Massachusetts General Hospital Building 120, 2nd avenue, Suite 103 Charlestown, MA 02129 Tel: 617-643-5078 (lab) 607-229-7096 (cell) On Dec 10, 2013, at 2:32 PM, Bruce Fischl wrote: go back and look at the dicoms I guess. Can you post these questions to the list so that others can answer? thanks Bruce On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D. wrote: How do I check if they are echoes of a multi-echo mprage? They should have... I mean all other subjects are fine (all others generated RMS automatically) besides these 2 subjects, I don't know if that's something wrong at the time with the data collection. On Dec 10, 2013, at 2:03 PM, Bruce Fischl wrote: you can use mri_average -sqr ... I believe, as long as these really are the echoes of a multi-echo mprage. Are you sure you didn't just point recon-all at the wrong series? It should have generated one automatically On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D. wrote: Hi Bruce, Only these two subjects didn't create the RMS automatically, I don't know why. How can I generate the RMS? Thanks, Noel On Dec 10, 2013, at 1:52 PM, Bruce Fischl wrote: Hi Noel what were the acquisitions? If they were multi-echo mprage than you will either have to generate the RMS or find the series that is the RMS (since it should have been generated automatically) cheers Bruce On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D. wrote: Hi, I'm trying to do recon-all for a file, and it gave me this multiple frame error message: #@# MotionCor Mon Nov 25 13:11:40 EST 2013 Found 1 runs /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/ orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/ orig/001.mgz has 4 frames If this is a multi-frame MEMPRAGE image, use mri_concat --rms to combine echo frames. Linux compute-0-73 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BHI_BJU-345_pre_lazar exited with ERRORS at Mon Nov 25 13:11:47 EST 2013 For more details, see
Re: [Freesurfer] qdec analysis with 2 covariates
i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the qdec output directory Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:42:37 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates Is there a cache.mri_glmfit-sim.log in the output folder? Can you send it to me? Also, please remember to post to the list. thanks! doug On 12/10/2013 02:30 PM, Jon Wieser wrote: FS version 5.3 - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:05:26 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates hmmm, it should be there. What version of FS are you using? On 12/10/2013 12:57 PM, Jon Wieser wrote: i was getting the values for the command terminal, when I press the find clusters and GOTo Max button on the qdec GUI. there is no file named cache.th20.abs.y.dat or something similar. i did a find command to list all the *abs*.dat files in the directory qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat these files contain: # CSD PDF/CDF # simtype null-z # anattype surface fsaverage lh # FixGroupSubjectArea 1 # merged 0 # contrastNA # seed1271277527 # thresh 1.30 # threshsign 0.00 # searchspace 74612.965197 # nullfwhm15.00 # varfwhm -1.00 # nrepetitions 1 # NOTE: nreps and nrepetitions are both valid for volume data. # NOTE: nreps is invalid (-1) for surface data to assure. # NOTE: backwards INcompatibility. # $Id: volcluster.c,v 1.50.2.1 2011/03/28 15:32:36 greve Exp $ # nreps -1 # FixSurfClusterArea 1 # $Id: surfcluster.c,v 1.26.2.2 2011/11/10 16:01:11 greve Exp $ # nbins 100 # BinNo MaxClustBin MaxClustPDF MaxClustCDF GRFCDFMaxSigBin MaxSigPDF MaxSigCDF 0 204.826004 0.000500 0.999500 0.998289 2.456050 0.000500 0.999500 1 220.348267 0.001800 0.997700 0.996805 2.811329 0.008100 0.991400 2 235.870529 0.004300 0.993400 0.994388 3.166609 0.022200 0.969200 3 251.392792 0.007100 0.986300 0.990673 3.521888 0.030300 0.938900 4 266.915039 0.015600 0.970700 0.985251 3.877167 0.028900 0.91 5 282.437317 0.017500 0.953200 0.977702 4.232447 0.022600 0.887400 6 297.959595 0.021400 0.931800 0.967628 4.587726 0.015200 0.872200 7 313.481842 0.033600 0.898200 0.954689 4.943005 0.012300 0.859900 8 329.004089 0.036100 0.862100 0.938634 5.298285 0.009800 0.850100 9 344.526367 0.038000 0.824100 0.919325 5.653563 0.007300 0.842800 10 360.048645 0.042500 0.781600 0.896747 6.008843 0.009200 0.833600 11 375.570892 0.05 0.731600 0.871009 6.364122 0.006900 0.826700 12 391.093140 0.043400 0.688200 0.842332 6.719401 0.007100 0.819600 13 406.615417 0.047300 0.640900 0.811034 7.074681 0.005500 0.814100 14 422.137695 0.050700 0.590200 0.777508 7.429960 0.005500 0.808600 15 437.659943 0.047400 0.542800 0.742195 7.785239 0.005200 0.803400 16 453.182190 0.044100 0.498700 0.705560 8.140518 0.004900 0.798500 17 468.704468 0.042700 0.456000 0.668070 8.495798 0.005100 0.793400 18 484.226746 0.040600 0.415400 0.630176 8.851077 0.006100 0.787300 19 499.748962 0.034900 0.380500 0.592300 9.206356 0.004800 0.782500 20 515.271240 0.032200 0.348300 0.554820 9.561636 0.003600 0.778900 21 530.793518 0.031400 0.316900 0.518067 9.916915 0.003400 0.775500 22 546.315796 0.032400 0.284500 0.482320 10.272194 0.004000 0.771500 23 561.838013 0.023800 0.260700 0.447809 10.627474 0.004800 0.766700 24 577.360291 0.026100 0.234600 0.414711 10.982753 0.004500 0.762200 25 592.882568 0.022700 0.211900 0.383160 11.338033 0.003300 0.758900 26 608.404846 0.017500 0.194400 0.353244 11.693312 0.003100 0.755800 27 623.927063
Re: [Freesurfer] qdec analysis with 2 covariates
OK, sorry, I thought qdec was running a script called mri_glmfit-sim but it appears to be running the correction internally. That means that you will have to run mri_glmfit-sim yourself, something like mri_glmfit-sim --glmdir glmdir --cache 1.3 abs doug On 12/10/2013 02:53 PM, Jon Wieser wrote: i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the qdec output directory Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:42:37 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates Is there a cache.mri_glmfit-sim.log in the output folder? Can you send it to me? Also, please remember to post to the list. thanks! doug On 12/10/2013 02:30 PM, Jon Wieser wrote: FS version 5.3 - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:05:26 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates hmmm, it should be there. What version of FS are you using? On 12/10/2013 12:57 PM, Jon Wieser wrote: i was getting the values for the command terminal, when I press the find clusters and GOTo Max button on the qdec GUI. there is no file named cache.th20.abs.y.dat or something similar. i did a find command to list all the *abs*.dat files in the directory qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat these files contain: # CSD PDF/CDF # simtype null-z # anattype surface fsaverage lh # FixGroupSubjectArea 1 # merged 0 # contrastNA # seed1271277527 # thresh 1.30 # threshsign 0.00 # searchspace 74612.965197 # nullfwhm15.00 # varfwhm -1.00 # nrepetitions 1 # NOTE: nreps and nrepetitions are both valid for volume data. # NOTE: nreps is invalid (-1) for surface data to assure. # NOTE: backwards INcompatibility. # $Id: volcluster.c,v 1.50.2.1 2011/03/28 15:32:36 greve Exp $ # nreps -1 # FixSurfClusterArea 1 # $Id: surfcluster.c,v 1.26.2.2 2011/11/10 16:01:11 greve Exp $ # nbins 100 # BinNo MaxClustBin MaxClustPDF MaxClustCDF GRFCDFMaxSigBin MaxSigPDF MaxSigCDF 0 204.826004 0.000500 0.999500 0.998289 2.456050 0.000500 0.999500 1 220.348267 0.001800 0.997700 0.996805 2.811329 0.008100 0.991400 2 235.870529 0.004300 0.993400 0.994388 3.166609 0.022200 0.969200 3 251.392792 0.007100 0.986300 0.990673 3.521888 0.030300 0.938900 4 266.915039 0.015600 0.970700 0.985251 3.877167 0.028900 0.91 5 282.437317 0.017500 0.953200 0.977702 4.232447 0.022600 0.887400 6 297.959595 0.021400 0.931800 0.967628 4.587726 0.015200 0.872200 7 313.481842 0.033600 0.898200 0.954689 4.943005 0.012300 0.859900 8 329.004089 0.036100 0.862100 0.938634 5.298285 0.009800 0.850100 9 344.526367 0.038000 0.824100 0.919325 5.653563 0.007300 0.842800 10 360.048645 0.042500 0.781600 0.896747 6.008843 0.009200 0.833600 11 375.570892 0.05 0.731600 0.871009 6.364122 0.006900 0.826700 12 391.093140 0.043400 0.688200 0.842332 6.719401 0.007100 0.819600 13 406.615417 0.047300 0.640900 0.811034 7.074681 0.005500 0.814100 14 422.137695 0.050700 0.590200 0.777508 7.429960 0.005500 0.808600 15 437.659943 0.047400 0.542800 0.742195 7.785239 0.005200 0.803400 16 453.182190 0.044100 0.498700 0.705560 8.140518 0.004900 0.798500 17 468.704468 0.042700 0.456000 0.668070 8.495798 0.005100 0.793400 18 484.226746 0.040600 0.415400 0.630176 8.851077 0.006100 0.787300 19 499.748962 0.034900 0.380500 0.592300 9.206356 0.004800 0.782500 20 515.271240 0.032200 0.348300 0.554820 9.561636 0.003600 0.778900 21 530.793518 0.031400 0.316900 0.518067 9.916915 0.003400 0.775500 22 546.315796 0.032400 0.284500 0.482320 10.272194 0.004000 0.771500 23 561.838013 0.023800 0.260700 0.447809
Re: [Freesurfer] T1 FLASH parameters for cortical thickness analyses
Hi Bruce, Thank you for the reply and the suggestions. So if I shorten the TE on the FLASH and lengthen the overall scan time, will that help ? I am specifically interested in the brain vol (minus CSF) for MS atrophy as well as cortical thickness analyses so I am keen to explore the possibility to extract both the measures from a single anatomical sequence. Please let me know. Thanks Rito - Original Message - From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Ritobrato Datta rida...@mail.med.upenn.edu Cc: free surfer freesurfer@nmr.mgh.harvard.edu Sent: Tue, 10 Dec 2013 13:42:05 -0500 (EST) Subject: Re: [Freesurfer] T1 FLASH parameters for cortical thickness analyses Hi Ri the sequence looks reasonable, although your TE of 5ms is somewhat long and will reduce CNR and SNR. Can you shorten it? I would think you should be able to. We looked at this for a while, and in the end the mprage outperformed FLASH in terms of cortical gray matter/cerebral white matter CNR/unit time. The FLASH scans were ok, but not as good as mprage. I think either is fine for ICV, although if you collect a lower fiip FLASH which will be PD weighted (e.g. a 5deg) then that will be an advantage for ICV. cheers Bruce On Tue, 10 Dec 2013, Ritobrato Datta wrote: Hi All, I have collected T1 3D FLASH on a subject and here are some details of the sequence, Manufacturer = SIEMENS StudyDescription = Neuro_3T^brain_3t SeriesDescription = Axial Global FLASH FA27 ManufacturersModelName = Verio ReferencedImageSequence = 1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835978\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835980\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835979 ScanningSequence = GR SequenceVariant = SP ScanOptions = SAT1 MRAcquisitionType = 3D SequenceName = *fl3d1 SliceThickness = 1 RepetitionTime = 20 EchoTime = 5 InversionTime = - NumberofAverages = 1 ImagingFrequency = 123.200338 ImagedNucleus = 1H EchoNumbers = 1 MagneticFieldStrength = 3 NumberofPhaseEncodingSteps = 192 EchoTrainLength = 1 PercentSampling = 100 PercentPhaseFieldofView = 75 PixelBandwidth = 179 DeviceSerialNumber = 40156 SoftwareVersions = syngo MR B17 ProtocolName = Axial Global FLASH FA27 TransmitCoilName = Body AcquisitionMatrix = 0\256\192\0 In-planePhaseEncodingDirection = ROW FlipAngle = 27 VariableFlipAngleFlag = N SAR = 0.19411263 My questions are the following - 1) Can I get reliable cortical thickness estimates using a T1 3D FLASH sequence at 3T Siemens TRIO ? 2) Which version of freesurfer is recommended ? 3) One reason, I collected T1 FLASH is I want to get whole brain volume and brain parenchymal fraction in Multiple sclerosis patients. But if freesurfer prefers MPRAGES over FLASH for cortical thickness, I am wondering how reliable are the standard MPRAGE sequences for calculation of whole brain volume and brain parenchymal fractions ? 4) I ran the recon on the FLASH using freesurfer 5.3 and it looks very decent but has anyone tested and optimized the parameters for the T1 FLASH sequence for cortical thickness estimations ? 5) If you can share your opinion and experiences in this topic and maybe point me to some references using flash and freesurfer for cortical thickness, that will be very helpful. Best 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] New features in TRACULA
Hi Anastasia, We discussed your paper at our lab meeting yesterday so this was perfect timing on the release of motion measures in your updated TRACULA. But I wasn't clear where the numbers are coming from in your new update. Is this from EDDY? eddy_correct? Some other registration step? Thanks, Ruth ___ 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] multiple frames error message for recon-all
it doesn't create it when it unpacks it - it is a separate series created
on the scanner. If you have the echoes in a single .mgz file named
echoes.mgz you would to:
foreach e (0 1 2 3)
mri_convert -nth $e echoes.mgz echo${e}.mgz
end
mri_average -sqr echo[0123].mgz rms.mgz
cheers
Bruce
On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D. wrote:
Thanks Bruce. I checked, it is multi-echo mprage, it's just when I unpack
it, it didn't automatically generate the RMS.
so can you walk me through when to do the mri-average-sqr?
So I just type the command:
unpacksdcmdir -src
/cluster/archive/304/siemens/Skyra-45407-20130822-092226-174000 -targ .
-scanonly unpacklogpre
Then it gives me:
Tue Dec 10 14:56:36 EST 2013
Log File is ./unpack.log
INFO: Logfile is ./unpack.log
SkipMoCo 0
Scanning source directory ...
INFO: summary file is ./dicomdir.sumfile
INFO: status file is ./parse.status
Scanning directory Tue Dec 10 14:56:36 EST 2013
mri_parse_sdcmdir --sortbyrun --d
/cluster/archive/304/siemens/Skyra-45407-20130822-092226-174000 --o
./dicomdir.sumfile --status ./parse.status
0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36
38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74
76 78 80 82 84 86 88 90 92 94 96 98 100
Done scanning Tue Dec 10 14:58:48 EST 2013
--
1 localizer ok 256 256 3 1
MR.1.3.12.2.1107.5.2.19.45407.2013082209234488137601798
2 localizer ok 256 256 3 1
MR.1.3.12.2.1107.5.2.19.45407.2013082209234486217101797
3 AAHead_Scout ok 160 160 128 1
MR.1.3.12.2.1107.5.2.19.45407.2013082209242568708801865
4 AAHead_Scout ok 162 162 5 1
MR.1.3.12.2.1107.5.2.19.45407.2013082209243010322103111
5 AAHead_Scout ok 162 162 3 1
MR.1.3.12.2.1107.5.2.19.45407.2013082209243010400603115
6 AAHead_Scout ok 162 162 3 1
MR.1.3.12.2.1107.5.2.19.45407.2013082209243010456303118
7 MEMPRAGE_tfl_mgh_multiecho_1mm_iso ok 256 256 176 4
MR.1.3.12.2.1107.5.2.19.45407.2013082209321083146803580
8 fMRI_resting_state ok 72 72 47 124
MR.1.3.12.2.1107.5.2.19.45407.2013082209330867404606382
How do I create the RMS?
Thanks,
Noel
---
Noel Yanki Chan, PhD
Department of Psychiatry Neuroscience
Laboratory of Sara Lazar, PhD
Harvard Medical School
Massachusetts General Hospital
Building 120, 2nd avenue, Suite 103
Charlestown, MA 02129
Tel: 617-643-5078 (lab) 607-229-7096 (cell)
On Dec 10, 2013, at 2:32 PM, Bruce Fischl wrote:
go back and look at the dicoms I guess. Can you post these
questions to the list so that others can answer?
thanks
Bruce
On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D. wrote:
How do I check if they are echoes of a multi-echo
mprage? They should
have... I mean all other subjects are fine (all
others generated RMS
automatically) besides these 2 subjects, I don't
know if that's something
wrong at the time with the data collection.
On Dec 10, 2013, at 2:03 PM, Bruce Fischl wrote:
you can use mri_average -sqr ... I believe, as
long as these
really are the echoes of a multi-echo mprage.
Are you sure you
didn't just point recon-all at the wrong
series? It should have
generated one automatically
On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D.
wrote:
Hi Bruce,
Only these two subjects didn't create the
RMS
automatically, I don't know
why. How can I generate the RMS?
Thanks,
Noel
On Dec 10, 2013, at 1:52 PM, Bruce Fischl
wrote:
Hi Noel
what were the acquisitions? If they
were
multi-echo mprage than
you will either have to generate the
RMS or
find the series that
is the RMS (since it should have
been generated
automatically)
cheers
Bruce
On Tue, 10 Dec 2013, Chan, Noel
Yan-Ki,Ph.D.
wrote:
Hi,
I'm trying to do recon-all for
a file,
and it gave
me this multiple frame
error message:
#@# MotionCor Mon Nov 25
13:11:40 EST
2013
Re: [Freesurfer] qdec analysis with 2 covariates
thanks, I ran mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs MTA_ADHD_MJ is my project file and has the results from qdec in it it has produced: lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat these files have 120 rows. each row has a thickness value s example 2.71869 2.52448 2.50450 2.53677 2.58363 2.50404 2.42116 2.61757 2.51820 2.59009 2.42524 2.72043 2.59479 2.38014 2.41052 2.58483 2.49214 2.45870 2.51685 2.62981 2.59232 it appears that there is the thickness for each subject in the files I would like to have the thickness value, for each cluster, for every subject we have 120 subjects, with about 40 clusters Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 2:30:31 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates OK, sorry, I thought qdec was running a script called mri_glmfit-sim but it appears to be running the correction internally. That means that you will have to run mri_glmfit-sim yourself, something like mri_glmfit-sim --glmdir glmdir --cache 1.3 abs doug On 12/10/2013 02:53 PM, Jon Wieser wrote: i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the qdec output directory Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:42:37 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates Is there a cache.mri_glmfit-sim.log in the output folder? Can you send it to me? Also, please remember to post to the list. thanks! doug On 12/10/2013 02:30 PM, Jon Wieser wrote: FS version 5.3 - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:05:26 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates hmmm, it should be there. What version of FS are you using? On 12/10/2013 12:57 PM, Jon Wieser wrote: i was getting the values for the command terminal, when I press the find clusters and GOTo Max button on the qdec GUI. there is no file named cache.th20.abs.y.dat or something similar. i did a find command to list all the *abs*.dat files in the directory qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat these files contain: # CSD PDF/CDF # simtype null-z # anattype surface fsaverage lh # FixGroupSubjectArea 1 # merged 0 # contrastNA # seed1271277527 # thresh 1.30 # threshsign 0.00 # searchspace 74612.965197 # nullfwhm15.00 # varfwhm -1.00 # nrepetitions 1 # NOTE: nreps and nrepetitions are both valid for volume data. #
Re: [Freesurfer] qdec analysis with 2 covariates
There should be a column for each cluster in contrast. Is that what you want? On 12/10/2013 04:37 PM, Jon Wieser wrote: thanks, I ran mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs MTA_ADHD_MJ is my project file and has the results from qdec in it it has produced: lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat these files have 120 rows. each row has a thickness value s example 2.71869 2.52448 2.50450 2.53677 2.58363 2.50404 2.42116 2.61757 2.51820 2.59009 2.42524 2.72043 2.59479 2.38014 2.41052 2.58483 2.49214 2.45870 2.51685 2.62981 2.59232 it appears that there is the thickness for each subject in the files I would like to have the thickness value, for each cluster, for every subject we have 120 subjects, with about 40 clusters Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 2:30:31 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates OK, sorry, I thought qdec was running a script called mri_glmfit-sim but it appears to be running the correction internally. That means that you will have to run mri_glmfit-sim yourself, something like mri_glmfit-sim --glmdir glmdir --cache 1.3 abs doug On 12/10/2013 02:53 PM, Jon Wieser wrote: i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the qdec output directory Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:42:37 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates Is there a cache.mri_glmfit-sim.log in the output folder? Can you send it to me? Also, please remember to post to the list. thanks! doug On 12/10/2013 02:30 PM, Jon Wieser wrote: FS version 5.3 - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:05:26 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates hmmm, it should be there. What version of FS are you using? On 12/10/2013 12:57 PM, Jon Wieser wrote: i was getting the values for the command terminal, when I press the find clusters and GOTo Max button on the qdec GUI. there is no file named cache.th20.abs.y.dat or something similar. i did a find command to list all the *abs*.dat files in the directory qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat these files contain: # CSD PDF/CDF # simtype null-z # anattype surface fsaverage lh # FixGroupSubjectArea 1 # merged 0 # contrastNA # seed1271277527 # thresh 1.30
Re: [Freesurfer] qdec analysis with 2 covariates
yes, that is what we want, but the files contain only 1-3 columns Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 3:44:50 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates There should be a column for each cluster in contrast. Is that what you want? On 12/10/2013 04:37 PM, Jon Wieser wrote: thanks, I ran mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs MTA_ADHD_MJ is my project file and has the results from qdec in it it has produced: lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat these files have 120 rows. each row has a thickness value s example 2.71869 2.52448 2.50450 2.53677 2.58363 2.50404 2.42116 2.61757 2.51820 2.59009 2.42524 2.72043 2.59479 2.38014 2.41052 2.58483 2.49214 2.45870 2.51685 2.62981 2.59232 it appears that there is the thickness for each subject in the files I would like to have the thickness value, for each cluster, for every subject we have 120 subjects, with about 40 clusters Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 2:30:31 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates OK, sorry, I thought qdec was running a script called mri_glmfit-sim but it appears to be running the correction internally. That means that you will have to run mri_glmfit-sim yourself, something like mri_glmfit-sim --glmdir glmdir --cache 1.3 abs doug On 12/10/2013 02:53 PM, Jon Wieser wrote: i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the qdec output directory Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:42:37 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates Is there a cache.mri_glmfit-sim.log in the output folder? Can you send it to me? Also, please remember to post to the list. thanks! doug On 12/10/2013 02:30 PM, Jon Wieser wrote: FS version 5.3 - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:05:26 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates hmmm, it should be there. What version of FS are you using? On 12/10/2013 12:57 PM, Jon Wieser wrote: i was getting the values for the command terminal, when I press the find clusters and GOTo Max button on the qdec GUI. there is no file named cache.th20.abs.y.dat or something similar. i did a find command to list all the *abs*.dat files in the directory qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat
Re: [Freesurfer] T1 FLASH parameters for cortical thickness analyses
Hi Rito shortening the TE wouldn't change the overall acquisition. If it's total brain volume you are interested in, you might consider getting the low flip FLASH in addition cheers Bruce On Tue, 10 Dec 2013, Ritobrato Datta wrote: Hi Bruce, Thank you for the reply and the suggestions. So if I shorten the TE on the FLASH and lengthen the overall scan time, will that help ? I am specifically interested in the brain vol (minus CSF) for MS atrophy as well as cortical thickness analyses so I am keen to explore the possibility to extract both the measures from a single anatomical sequence. Please let me know. Thanks Rito - Original Message - From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Ritobrato Datta rida...@mail.med.upenn.edu Cc: free surfer freesurfer@nmr.mgh.harvard.edu Sent: Tue, 10 Dec 2013 13:42:05 -0500 (EST) Subject: Re: [Freesurfer] T1 FLASH parameters for cortical thickness analyses Hi Ri the sequence looks reasonable, although your TE of 5ms is somewhat long and will reduce CNR and SNR. Can you shorten it? I would think you should be able to. We looked at this for a while, and in the end the mprage outperformed FLASH in terms of cortical gray matter/cerebral white matter CNR/unit time. The FLASH scans were ok, but not as good as mprage. I think either is fine for ICV, although if you collect a lower fiip FLASH which will be PD weighted (e.g. a 5deg) then that will be an advantage for ICV. cheers Bruce On Tue, 10 Dec 2013, Ritobrato Datta wrote: Hi All, I have collected T1 3D FLASH on a subject and here are some details of the sequence, Manufacturer = SIEMENS StudyDescription = Neuro_3T^brain_3t SeriesDescription = Axial Global FLASH FA27 ManufacturersModelName = Verio ReferencedImageSequence = 1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835978\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835980\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835979 ScanningSequence = GR SequenceVariant = SP ScanOptions = SAT1 MRAcquisitionType = 3D SequenceName = *fl3d1 SliceThickness = 1 RepetitionTime = 20 EchoTime = 5 InversionTime = - NumberofAverages = 1 ImagingFrequency = 123.200338 ImagedNucleus = 1H EchoNumbers = 1 MagneticFieldStrength = 3 NumberofPhaseEncodingSteps = 192 EchoTrainLength = 1 PercentSampling = 100 PercentPhaseFieldofView = 75 PixelBandwidth = 179 DeviceSerialNumber = 40156 SoftwareVersions = syngo MR B17 ProtocolName = Axial Global FLASH FA27 TransmitCoilName = Body AcquisitionMatrix = 0\256\192\0 In-planePhaseEncodingDirection = ROW FlipAngle = 27 VariableFlipAngleFlag = N SAR = 0.19411263 My questions are the following - 1) Can I get reliable cortical thickness estimates using a T1 3D FLASH sequence at 3T Siemens TRIO ? 2) Which version of freesurfer is recommended ? 3) One reason, I collected T1 FLASH is I want to get whole brain volume and brain parenchymal fraction in Multiple sclerosis patients. But if freesurfer prefers MPRAGES over FLASH for cortical thickness, I am wondering how reliable are the standard MPRAGE sequences for calculation of whole brain volume and brain parenchymal fractions ? 4) I ran the recon on the FLASH using freesurfer 5.3 and it looks very decent but has anyone tested and optimized the parameters for the T1 FLASH sequence for cortical thickness estimations ? 5) If you can share your opinion and experiences in this topic and maybe point me to some references using flash and freesurfer for cortical thickness, that will be very helpful. Best 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec analysis with 2 covariates
So one of the contrasts has 40 clusters in the summary file but the y.ocn.dat file only has a few columns? On 12/10/2013 04:54 PM, Jon Wieser wrote: yes, that is what we want, but the files contain only 1-3 columns Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 3:44:50 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates There should be a column for each cluster in contrast. Is that what you want? On 12/10/2013 04:37 PM, Jon Wieser wrote: thanks, I ran mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs MTA_ADHD_MJ is my project file and has the results from qdec in it it has produced: lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat these files have 120 rows. each row has a thickness value s example 2.71869 2.52448 2.50450 2.53677 2.58363 2.50404 2.42116 2.61757 2.51820 2.59009 2.42524 2.72043 2.59479 2.38014 2.41052 2.58483 2.49214 2.45870 2.51685 2.62981 2.59232 it appears that there is the thickness for each subject in the files I would like to have the thickness value, for each cluster, for every subject we have 120 subjects, with about 40 clusters Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 2:30:31 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates OK, sorry, I thought qdec was running a script called mri_glmfit-sim but it appears to be running the correction internally. That means that you will have to run mri_glmfit-sim yourself, something like mri_glmfit-sim --glmdir glmdir --cache 1.3 abs doug On 12/10/2013 02:53 PM, Jon Wieser wrote: i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the qdec output directory Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:42:37 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates Is there a cache.mri_glmfit-sim.log in the output folder? Can you send it to me? Also, please remember to post to the list. thanks! doug On 12/10/2013 02:30 PM, Jon Wieser wrote: FS version 5.3 - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:05:26 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates hmmm, it should be there. What version of FS are you using? On 12/10/2013 12:57 PM, Jon Wieser wrote: i was getting the values for the command terminal, when I press the find clusters and GOTo Max button on the qdec GUI. there is no file named cache.th20.abs.y.dat or something similar. i did a find command to list all the *abs*.dat files in the directory qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat
Re: [Freesurfer] qdec analysis with 2 covariates
which contrast are you looking at in QDEC? Also, what is the voxel-wise threshold in QDEC? The value I gave in the command below is 1.3 but I got that from one of your CSD files. On 12/10/2013 05:10 PM, Jon Wieser wrote: HI doug, no, the summary files in the contrasts have the same # of cluster as the columns in their OCN.dat \ the 40 cluster are seen in qdec when I run the find cluster and Goto max button. most of these clusters go away in qdec when I run the montecarlo simulation Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 4:03:06 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates So one of the contrasts has 40 clusters in the summary file but the y.ocn.dat file only has a few columns? On 12/10/2013 04:54 PM, Jon Wieser wrote: yes, that is what we want, but the files contain only 1-3 columns Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 3:44:50 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates There should be a column for each cluster in contrast. Is that what you want? On 12/10/2013 04:37 PM, Jon Wieser wrote: thanks, I ran mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs MTA_ADHD_MJ is my project file and has the results from qdec in it it has produced: lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat these files have 120 rows. each row has a thickness value s example 2.71869 2.52448 2.50450 2.53677 2.58363 2.50404 2.42116 2.61757 2.51820 2.59009 2.42524 2.72043 2.59479 2.38014 2.41052 2.58483 2.49214 2.45870 2.51685 2.62981 2.59232 it appears that there is the thickness for each subject in the files I would like to have the thickness value, for each cluster, for every subject we have 120 subjects, with about 40 clusters Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 2:30:31 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates OK, sorry, I thought qdec was running a script called mri_glmfit-sim but it appears to be running the correction internally. That means that you will have to run mri_glmfit-sim yourself, something like mri_glmfit-sim --glmdir glmdir --cache 1.3 abs doug On 12/10/2013 02:53 PM, Jon Wieser wrote: i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the qdec output directory Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:42:37 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates Is there a cache.mri_glmfit-sim.log in the output folder? Can you send it to me? Also, please remember to post to the list. thanks! doug On 12/10/2013 02:30 PM, Jon Wieser wrote: FS version 5.3 - Original Message -
Re: [Freesurfer] qdec analysis with 2 covariates
Hi Doug I'm looking at the effect of MJ usage, the effect of whetherthe subject has AHDH, and the interaction between MJ usage and ADHD our threshold is 1.3 i have attahced our qdec.table.dat file we are also looking at age and gender as covariates Jon Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 4:20:30 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates which contrast are you looking at in QDEC? Also, what is the voxel-wise threshold in QDEC? The value I gave in the command below is 1.3 but I got that from one of your CSD files. On 12/10/2013 05:10 PM, Jon Wieser wrote: HI doug, no, the summary files in the contrasts have the same # of cluster as the columns in their OCN.dat \ the 40 cluster are seen in qdec when I run the find cluster and Goto max button. most of these clusters go away in qdec when I run the montecarlo simulation Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 4:03:06 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates So one of the contrasts has 40 clusters in the summary file but the y.ocn.dat file only has a few columns? On 12/10/2013 04:54 PM, Jon Wieser wrote: yes, that is what we want, but the files contain only 1-3 columns Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 3:44:50 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates There should be a column for each cluster in contrast. Is that what you want? On 12/10/2013 04:37 PM, Jon Wieser wrote: thanks, I ran mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs MTA_ADHD_MJ is my project file and has the results from qdec in it it has produced: lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat these files have 120 rows. each row has a thickness value s example 2.71869 2.52448 2.50450 2.53677 2.58363 2.50404 2.42116 2.61757 2.51820 2.59009 2.42524 2.72043 2.59479 2.38014 2.41052 2.58483 2.49214 2.45870 2.51685 2.62981 2.59232 it appears that there is the thickness for each subject in the files I would like to have the thickness value, for each cluster, for every subject we have 120 subjects, with about 40 clusters Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 2:30:31 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates OK, sorry, I thought qdec was running a script called mri_glmfit-sim but it appears to be running the correction internally. That means that you will have to run mri_glmfit-sim yourself, something like mri_glmfit-sim --glmdir glmdir --cache 1.3 abs doug On 12/10/2013 02:53 PM, Jon Wieser wrote: i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the qdec
Re: [Freesurfer] part of GM missing
Dear all, What I mean is the boundary of pial is incorrect when I check that by this tkmedit subject brainmask.mgz -surfs I want to know how to change the boundary of the pial. Thanks. All the best. 2013-12-11 Rujing Zha 发件人：Rujing Zha zh...@mail.ustc.edu.cn 发送时间：2013-12-10 22:51 主题：[Freesurfer] part of GM missing 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Dear all, In tkmedit brainmask.mgz -surfs, there are a bit of GM part missing. I want to know how to paint the voxels to lable it as GM. And then run recon-all in a specific style to reconstruct the surfs. Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ 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] Do these bvec and bval files match?
Hi Emad - The bvecs file that you sent is formatted so that each column is a gradient vector. The first column is [0, 0, 0] and this corresponds to a b-value equal to 0 in the bvals file. So that's fine. You'll just have to download the latest update to tracula to be able to use this column-wise format, as previously the bvecs file had to be formatted in rows. a.y On Tue, 10 Dec 2013, Emad Ahmadi wrote: Hello, I'm using TRACULA to analyze images obtained by a non-Siemens scanner, and I'm using dcm2niigui app to generate bvec and bval files from DICOMs. My question is whether or not the attached bvec and bval files match, because the 0 bval is the first entry while the 0,0,0 bvec is somewhere in the middle. If they don't, how should I generate the correct bval/bvec files from dicoms? Lots of thanks, Emad ___ 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] New features in TRACULA
Hi Ruth - Glad to hear this is useful to you. The rotation and translation parameters are extracted from the affine registration of each DWI volume to the first volume, which in trac-all is performed by eddy_correct. a.y On Tue, 10 Dec 2013, Ruth Carper wrote: Hi Anastasia, We discussed your paper at our lab meeting yesterday so this was perfect timing on the release of motion measures in your updated TRACULA. But I wasn't clear where the numbers are coming from in your new update. Is this from EDDY? eddy_correct? Some other registration step? Thanks, Ruth ___ 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.
