Re: [Freesurfer] Correction of registration in preproc-sess stream
Dear Doug, I have tested the various options of register-sess. The result was a succesful registration of the functional to the anatomical image. This registration with register-sess is performed after preproc-sess failed to achieve a proper registration. The register.dof6.dat file is updated by register-sess. I would like to ask a last thing just in order to make it definite. Can I now use those data for example with selxavg3-sess in order to compute the activated areas for this subject? Greets pfannmoe On Tue, 05 Jun 2012 18:30:42 -0400 Douglas Greve gr...@nmr.mgh.harvard.edu wrote: You can't do directly from preproc-sess, but you can do it from register-sess if you have an additional whole brain acquisition in the same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc) as long as it is whole brain. If your anatomical was acquired in the same session, then it is even easier because you can run register-sess with the -init-header option (instead of using fsl or spm). This assumes that the subject did not move more than 5mm between EPI and MPRAGE (usually the case). Let me know if this works for you. doug On 6/5/12 6:03 AM, Jörg Pfannmöller wrote: Dear Doug, I am having a partial field of view and a full brain scan. How can I integrate the results in the preproc-sess sequence in order to complete the preprocessing correctly? Cheers pfannmoe On Mon, 04 Jun 2012 11:42:32 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: You can try running register-sess outside of preproc-sess, something like register-sess -s session -fsd bold -per-run -init-spm before you do that, you need to have spm5 and matlab, and change your matlab/startup.m to add the spm5 path path(path,'/usr/pubsw/common/spm/spm5'); doug ps. Is this whole brain coverage or are you chopping off some of the brain On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote: Dear Doug, indeed the initialization fails. I was able to initiate bbregister manually, giving a good registration result. Can you give me a hint how to modify the registration and keeping the preproc-sess stream intact? Cheers pfannmoe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jörg Pfannmöller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] DTI question
Not sure if this is the simplest way but mri_convert --split, followed by mri_concat, should do it. You'll also have to remove the respective gradient directions from the gradient file. Hope this helps, a.y On Wed, 27 Jun 2012, Drottar, Marie wrote: I have a DTI dataset with 10 b0 and gradient 30 directions. I would like to remove one or two volumes from the dataset and then repackage the data. How do I do this? thank you Marie Drottar, MA Research Assistant Division of Newborn Medicine Fetal-Neonatal Neuroimaging Developmental Science Center Boston Childrens Hospital 1 Autumn St Boston, MA 02115 http://childrenshospital.org/FNNDSC ___ 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] Correction of registration in preproc-sess stream
You should run preproc-sess again to make sure that all the files that need to be updated after the registration are properly updated. This should not change the registration -- it should just look at the time stamps of the files and update any that need updating. However, if the files earlier in the stream were changed at some point, then it might try to regenerate the registration, so just in case make a backup of your registration files before running preproc-sess. doug On 06/27/2012 08:08 AM, Jörg Pfannmöller wrote: Dear Doug, I have tested the various options of register-sess. The result was a succesful registration of the functional to the anatomical image. This registration with register-sess is performed after preproc-sess failed to achieve a proper registration. The register.dof6.dat file is updated by register-sess. I would like to ask a last thing just in order to make it definite. Can I now use those data for example with selxavg3-sess in order to compute the activated areas for this subject? Greets pfannmoe On Tue, 05 Jun 2012 18:30:42 -0400 Douglas Grevegr...@nmr.mgh.harvard.edu wrote: You can't do directly from preproc-sess, but you can do it from register-sess if you have an additional whole brain acquisition in the same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc) as long as it is whole brain. If your anatomical was acquired in the same session, then it is even easier because you can run register-sess with the -init-header option (instead of using fsl or spm). This assumes that the subject did not move more than 5mm between EPI and MPRAGE (usually the case). Let me know if this works for you. doug On 6/5/12 6:03 AM, Jörg Pfannmöller wrote: Dear Doug, I am having a partial field of view and a full brain scan. How can I integrate the results in the preproc-sess sequence in order to complete the preprocessing correctly? Cheers pfannmoe On Mon, 04 Jun 2012 11:42:32 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: You can try running register-sess outside of preproc-sess, something like register-sess -s session -fsd bold -per-run -init-spm before you do that, you need to have spm5 and matlab, and change your matlab/startup.m to add the spm5 path path(path,'/usr/pubsw/common/spm/spm5'); doug ps. Is this whole brain coverage or are you chopping off some of the brain On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote: Dear Doug, indeed the initialization fails. I was able to initiate bbregister manually, giving a good registration result. Can you give me a hint how to modify the registration and keeping the preproc-sess stream intact? Cheers pfannmoe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Correction of registration in preproc-sess stream
P.S.:I executed the following sequence to achieve the first level analysis with a correct registration. preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage lhrh -mni305 -fwhm 0 -per-run register-sess -s session_id -fsd bold -per-run -init-header preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -noreg -regfile session_id/bold/001/register.dof6.dat -force selxavg3-sess -s session_id -analysis stim.sm0.lh -no-preproc As far as I can see this is the right procedure. Do you agree or is there another or simpler way to correct the registration and proceed with a first level analysis? ___ 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] Hippocampal segmentation
Dear FreesurfersI'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts...If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields?I'm guessing not, but I wanna be sure. Because, as I've looked the -hippo-subfields recon seems to not modify the whole brain segmentation, am I right?second, when I apply the kvlQuantifyHippocampalSubfieldSegmentations.sh I do obtain two txt files containing such segmentation of the 8 hippocampal subfields, but at the beggining it appear a field for the left and right hippocampus, but I don't know exactly what does this column represents, because if I sum the other colums the subfield sums are so much bigger than the hippocampus field; i.e.volume_in_number_of_voxels Left-Hippocampus left_presubiculum left_CA1 left_CA2-3 left_fimbria left_subiculum left_CA4-DG left_hippocampal_fissurec_12_hipo 3789.97 3215.08 2654.65 7705.2 336.857 4841.63 4158.49 356.626and last. Do I need to somehow do some partial volume corrections to this output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw on the page that the output is 0.5*0.5*0.5mm^3. Many thanks in advanced,Gabriel ___ 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] DODS, DOSS, and interactions
Freesurfers- Question, when looking for interactions to justify using DOSS say i am looking at cortical thickness and i have two discrete variables (G1 and G2) and 4 continious variables (V1, V2, V3, V4). My thinking is that i should look to see if there are interactions with the groups and each individual variable. However what if it is likely that an interaction of G1, G2, and V1 can be explained by V2? Michael -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkrue...@gmail.com (262)-483-7449 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] error running FS on mac
Hi, I just installed Freesurfer on my Mac Lion. When I ran recon-all, I got the following error. Can't locate MNI/Startup.pm in @INC (@INC contains:) at Applications/freesurfer/mni/bin/nu_coorect line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. Has this occurred to anyone before? How to fix it? Thanks DJ ___ 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] DODS, DOSS, and interactions
If the covariates are collinear, then you can't properly estimate the model. They are collinear if they explain the variance of each other. I would first test for the relationship of your covariates before putting them into the model as you don't want the covariates to be collinear. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Wed, Jun 27, 2012 at 3:42 PM, mdkrue...@uwalumni.com mdkrue...@uwalumni.com wrote: Freesurfers- Question, when looking for interactions to justify using DOSS say i am looking at cortical thickness and i have two discrete variables (G1 and G2) and 4 continious variables (V1, V2, V3, V4). My thinking is that i should look to see if there are interactions with the groups and each individual variable. However what if it is likely that an interaction of G1, G2, and V1 can be explained by V2? Michael -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkrue...@gmail.com (262)-483-7449 ___ 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.
[Freesurfer] selxavg3-sess error
Hello, I'm trying to run selxavg3-sess with FS v4.5 for an FIR analysis where each trial is modeled as a separate condition. The command works smoothly for the majority of subjects, but for 2 different subjects, it exits with the following error: Saving X matrix to /home/sam/fMRIDATA/samstudies/SoCo/SoCo10/bold/Logit/Xtmp.mat XCond = 12220.6 (normalized) ERROR: design is ill-conditioned -- ERROR: fast_selxavg3() failed\n details: I do not definite any contrasts, as I'm only running this command to generate trial specific betas for a separate analysis. Each trial lasts 18 seconds, followed by 4 seconds of fixation. Here is what part of a paradigm file looks like (the paradigm files are identical for all subjects): 4 1 18 1 22 0 4 1 26 2 18 1 44 0 4 1 48 3 18 1 66 0 4 1 70 4 18 1 88 0 4 1 92 5 18 1 110 0 4 1 114 6 18 1 132 0 4 1 136 7 18 1 154 0 4 1 here are the analysis.cfg and .info files: analysis analysis_name TR 2 fsdbold funcstem fmcsm4 tpexclude parnameFIR_logit.par designtype event-related nconditions 96 -timewindow 20 -prestim 2 -acfbins 10 -fix-acf -noautostimdur -no-fsv3-st2fir -no-fsv3-whiten -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 the command which throws the error: selxavg3-sess -analysis analysis_name -s subject_name The strange part for me is that this only seems to be a problem with a couple subjects, despite the fact all the paradigm files are identical. After looking through the mailing archive, I tried playing around with the prestim window, but even it if is = 0, there is 1 subject that exits with an error when I run selxavg3-sess. Do you know what might be going on? Any guidance would be appreciated. Thanks, Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] qdec Error
Hi, I am in the testing process of Freesurfer on a 64-bit Ubuntu installed personal computer. However when I run the qdec command as suggested in the testing stages I receive the following error. qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Please let me know a solution to fix this issue. Thank you for all you help. Mohammed Goryawala ___ 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.
