Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions
Sorry that I keep on asking questions but I want to know if using a model can significantly increase the chance of getting a significant response. As far as I see for the positive peak, when I use a model (e.g. gamma model or spmhrf), I see a more significant response compared to when I use the FIR model. Is it correct? If true, then the same might be correct for the negative peak. P.S.: To be more clear, I am talking about the response maps relative to the baseline. On Apr 10, 2013 6:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: yes, that is what you want. The only other way that comes to mind is to model each event type as two event types one delayed relative to the other. Then model the responseto each as a gamma. If the delay is right, then the first gamma should model the main positive response and the second gamma will model the negative response. both will be independent from the other. doug On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu wrote: I think I figured it out but I want to double check. I am generating group-average map for my subjects using isxconcat-sess command which generates ces maps for each time frame. I think these maps are what I wanted. Right? If you still have other solutions that you think may generate more reliable results, I am eager to know. For instance, is there anyway to fit a model as we do for spmhrf or fslhrf, but just for the negative peak? Regards That's the problem Doug. I have already generated the FIR model but how can I show the sig MAP for one particulat time point. What are the other ways? On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu**wrote: Hi Shahin, there are several ways that you could do it. The one that immediately comes to mind is to use an FIR and then test for a difference at a particular post stimulus time point. doug On 04/10/2013 03:54 PM, SHAHIN NASR wrote: Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak of activity) between two conditions independent from the positive peak. Is there anyway, to generate this map? P.S.: Please note that I need a map and not a time course graph. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting http://**surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html h**ttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.*** *edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Surfaces to *native* space
Dear all, I think my issue is quite related to this one (if not duplicated, sorry in that case): https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027622.html As Shani, I used bbregister to coregister diffusion images to anatomical: bbregister --s OE0_T1 --mov DTI_b0_brain.nii.gz --reg dti2anat.dat --dti --init-fsl Then, I visually checked the outcome and resampled the T1 to DTI space: tkregister2 --mov DTI_b0.nii.gz --reg dti2anat.dat --surf mri_vol2vol --mov DTI_b0.nii.gz --targ OE0_T1/mri/T1.mgz --reg dti2anat.dat --o T1-to-DTI.nii.gz --inv tkregister2 --mov T1-to-DTI.nii.gz --targ DTI_b0.nii.gz --reg T1-to-DTI.nii.gz.reg Everything looks fine, but I cannot get the pial and white surfaces into dti space (please note the --reg-inv param and the ref volume DTI_b0.nii.gz, that should be important IMHO): mri_surf2surf --s OE0_T1 --sval-xyz white --reg-inv dti2anat.dat DTI_b0.nii.gz --tval lh.white.dti --tval-xyz --hemi lh There seems to exist an orientation problem when trying to visualize the surface tkmedit -f DTI_b0.nii.gz -surface lh.white.dti I also applied the solution that Douglas recommended Shani, without good results :(. Any light on this would be of the highest interest for me :D Thanks, Oscar -- Oscar Esteban PhD Student / Researcher Biomedical Image Technologies (BIT), UPM ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid (Spain) +34 915 495 700 ext.4234 Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5 ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland ___ 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] mgz to dicom
Hi All, Is there any tool,which can convert mgz files to Dicom? In Thanks chikku ___ 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] DTI: problems with (high) FA values
Hi Douge, In your last reply to my email (that contained questions regarding some really high FA values - see recent emails below), u asked me to write u the first value in register.dat.mincost - I'm copying the line I have: 0.280554 140.210312 156.795241 11.152485 Does this takes us one step further towards understanding the problem and its solution ? Thanks for your time, Rotem On 04/07/2013 06:48 AM, Rotem Saar wrote: Hi Doug, Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ? *yes, the ventricles look too high* When I first run the script, I got all values and looked the the CC - it looked fine. Then, I wanted to validate with some other regions, just to show that I got the appropriate (low) FA values for regions I don't expect to see high values in - and things looked odd (too high). I remember Bruce also writing me that the values seems a little high, but we didn't further discuss. I read the following this link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual The CC has an average FA of about 0.75, gyral parcellations are about 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as expected because the CC is highly directional with no crossing fibers so we would expect the CC to have the highest FA. The gyral white matter is also directional but has fibers crossing in them, so one expects the FA to be lower than CC. The gray matter (putamen) is still lower. The ventricle has no fibers, so we expect it to have the lowest FA. All my values are above 0.4 Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/ subjects/Rotem_try/mri/wmparc.mgz why do I get 182 regions ? in my wmparc.stats I have only 70... The wmparc includes all the subcortical and cortical regions too, but only the WM regions are reported in the wmparc.stats file. *To only report the WM regions, add to mri_segstats --ctab $FREESURFER_HOME/**WMParcStatsLUT.txt* I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help. *I don't know either. If I had to guess, I'd say it is a registration problem. What is the first value in register.dat.mincost?* doug Attached is the table again, Thanks Rotem The values look about right in the table. Your pipeline looks ok, thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output of mri_vol2vol (fa_FOLDER-NAME.nii). doug On 03/17/2013 02:16 AM, Rotem Saar wrote: Hi all, I run into somthing that seems odd to me and wanted to consult - I run the following script for getting the FA values from my DTI scans: 1) dt_recon --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I1.dcm --s FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec 2) tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii -fthresh 0.2 -fmax 1 4) mri_vol2vol --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s FOLDER-NAME --interp nearest --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat 5) tkregister2 --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg 6) mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii --sum /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME I got a table with all the FA values (see attached), for each segment, but I suspect a problem: I think that the values are too high (I set the threshold to 0.2-1), am I right ? Can u guide me regarding what I can do to solve the problem ? in addition I attached a figure of the corpus-callosum, in which I'm interested -
Re: [Freesurfer] mgz to dicom
Sorry, we don't write dicom usually, just read it Bruce On Apr 11, 2013, at 8:27 AM, Varghese Chikku chik...@tcd.ie wrote: Hi All, Is there any tool,which can convert mgz files to Dicom? In Thanks chikku ___ 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] merging dti data
Those commands were given to me by Anastasia. they work fine for merging two whole brain datasets. jon - Original Message - From: Douglas Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 10, 2013 10:13:05 PM Subject: Re: [Freesurfer] merging dti data Hi Jon, I don't know how to make this work, but I'm sure that those commands will not do it. Sorry:( doug On 4/10/13 1:13 PM, Jon Wieser wrote: we captured some dti data. there were 2 runs. we acquired in the axial plane, 2mm slice thickness the first run captured the lower half of the brain, slice locations: I56-S20, and the second run captured the upper half of the brain S16-S92. i have made briks from each of these runs. I can convert the briks to nifti files I want to merge the nifti files together to analyze the data in tracula In the past i have merged data from two dti runs, but each run have covered the entire brain, with the following commands mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz would it work to concat the two half brain niftis into one file and analyze that with tracula? (I will concat the bvec and bvals files too) would this cause problems doing it this way? Thanks Jon ___ 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. -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Transform SMOOTHWM to DTI B0
Hi all, I want to transform the Freesurfer Smoothwm surfaces to DTI B0 space. I found http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms but this describes transforming the B0 to T1 space and then match the surfaces. I don't want to change the DTI B0 image. What is the best way to do that? Thank you very much! Daniel -- Daniel Haehn FNNDSC / BCH +1.857.218.5140 ___ 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] Transform SMOOTHWM to DTI B0
hi dan, if you use bbregister to match the DTI b0 to freesurfer space, then you can transform the surface back (no guarantees on the tesselations though i think). the only additional component here would be a tkr transform that's based on the conformed space. i might even have some python code lying around to do this. i'll take a look. cheers, satra On Thu, Apr 11, 2013 at 10:40 AM, Daniel Haehn daniel.ha...@childrens.harvard.edu wrote: Hi all, I want to transform the Freesurfer Smoothwm surfaces to DTI B0 space. I found http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms but this describes transforming the B0 to T1 space and then match the surfaces. I don't want to change the DTI B0 image. What is the best way to do that? Thank you very much! Daniel -- Daniel Haehn FNNDSC / BCH +1.857.218.5140 ___ 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] Transform SMOOTHWM to DTI B0
Hi Satra, I have been trying to do that too. Do you have it as Nipy code? Thanks. Shantanu On Thu, April 11, 2013 10:53 am, Satrajit Ghosh wrote: hi dan, if you use bbregister to match the DTI b0 to freesurfer space, then you can transform the surface back (no guarantees on the tesselations though i think). the only additional component here would be a tkr transform that's based on the conformed space. i might even have some python code lying around to do this. i'll take a look. cheers, satra On Thu, Apr 11, 2013 at 10:40 AM, Daniel Haehn daniel.ha...@childrens.harvard.edu wrote: Hi all, I want to transform the Freesurfer Smoothwm surfaces to DTI B0 space. I found http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms but this describes transforming the B0 to T1 space and then match the surfaces. I don't want to change the DTI B0 image. What is the best way to do that? Thank you very much! Daniel -- Daniel Haehn FNNDSC / BCH +1.857.218.5140 ___ 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 -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] merging dti data
yes, they work for whole brain, but not if you have two brain halves. You might be able to do something in matlab. I assume the gradient direction order was the same for both slabs? doug On 4/11/13 10:36 AM, Jon Wieser wrote: Those commands were given to me by Anastasia. they work fine for merging two whole brain datasets. jon - Original Message - From: Douglas Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 10, 2013 10:13:05 PM Subject: Re: [Freesurfer] merging dti data Hi Jon, I don't know how to make this work, but I'm sure that those commands will not do it. Sorry:( doug On 4/10/13 1:13 PM, Jon Wieser wrote: we captured some dti data. there were 2 runs. we acquired in the axial plane, 2mm slice thickness the first run captured the lower half of the brain, slice locations: I56-S20, and the second run captured the upper half of the brain S16-S92. i have made briks from each of these runs. I can convert the briks to nifti files I want to merge the nifti files together to analyze the data in tracula In the past i have merged data from two dti runs, but each run have covered the entire brain, with the following commands mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz would it work to concat the two half brain niftis into one file and analyze that with tracula? (I will concat the bvec and bvals files too) would this cause problems doing it this way? Thanks Jon ___ 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] Autoreg-sess and mri_surf2vol
Hi, My name is Lucille and I'm really new with Freesurfer : My questions are very basic, sorry. I just start a project in segmentation of cerebrum. For converting a surface in volume. I would like to use mri_surf2vol but for that I need a volume registration file . For creating that file, I would use autoreg-sess. In documentation, it is said that : 'The volume registration file contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume' My question is : what here, represent the anatomical reference ? The functionnal volume ? Secondly, for autoreg-sess, the arguments are the subject name and the subject directory. I think the registration I need to create must be between my 2 volumes, so should I use the subject name and subject directory for my 2 subjects ? Sorry,I am really messed... Cheers Lucille ___ 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] merging dti data
the gradients were the same for each slab. What is the difficulty with runnning the merged brain halves in tracula? I have another to do it that I am going to try. I made AFNI Brik's of the two slabs, and merged them together into one AFNI brik with the AFNI command 3dZcat. I made a nifti file from the merged afni brik. i will try running tracula on the merged nifti file. Jon - Original Message - From: Douglas Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, April 11, 2013 9:56:53 AM Subject: Re: [Freesurfer] merging dti data yes, they work for whole brain, but not if you have two brain halves. You might be able to do something in matlab. I assume the gradient direction order was the same for both slabs? doug On 4/11/13 10:36 AM, Jon Wieser wrote: Those commands were given to me by Anastasia. they work fine for merging two whole brain datasets. jon - Original Message - From: Douglas Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 10, 2013 10:13:05 PM Subject: Re: [Freesurfer] merging dti data Hi Jon, I don't know how to make this work, but I'm sure that those commands will not do it. Sorry:( doug On 4/10/13 1:13 PM, Jon Wieser wrote: we captured some dti data. there were 2 runs. we acquired in the axial plane, 2mm slice thickness the first run captured the lower half of the brain, slice locations: I56-S20, and the second run captured the upper half of the brain S16-S92. i have made briks from each of these runs. I can convert the briks to nifti files I want to merge the nifti files together to analyze the data in tracula In the past i have merged data from two dti runs, but each run have covered the entire brain, with the following commands mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz would it work to concat the two half brain niftis into one file and analyze that with tracula? (I will concat the bvec and bvals files too) would this cause problems doing it this way? Thanks Jon ___ 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. -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Autoreg-sess and mri_surf2vol
Hi Lucille what do you mean by converting a surface to the volume? What do you want to do with it? What volume would you like to convert it to? cheers Bruce On Thu, 11 Apr 2013, Lucille Deroche wrote: Hi, My name is Lucille and I'm really new with Freesurfer : My questions are very basic, sorry. I just start a project in segmentation of cerebrum. For converting a surface in volume. I would like to use mri_surf2vol but for that I need a volume registration file . For creating that file, I would use autoreg-sess. In documentation, it is said that : 'The volume registration file contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume' My question is : what here, represent the anatomical reference ? The functionnal volume ? Secondly, for autoreg-sess, the arguments are the subject name and the subject directory. I think the registration I need to create must be between my 2 volumes, so should I use the subject name and subject directory for my 2 subjects ? Sorry,I am really messed... Cheers Lucille ___ 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] Autoreg-sess and mri_surf2vol
Hi Bruce, In fact, have 2 differents surfaces of pial surface. I would like to save my surfaces in volume to be able to calculate the dice score between the two. Cheers Lucille De : Bruce Fischl fis...@nmr.mgh.harvard.edu À : Lucille Deroche lucilledero...@yahoo.fr Cc : freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Envoyé le : Jeudi 11 avril 2013 11h18 Objet : Re: [Freesurfer] Autoreg-sess and mri_surf2vol Hi Lucille what do you mean by converting a surface to the volume? What do you want to do with it? What volume would you like to convert it to? cheers Bruce On Thu, 11 Apr 2013, Lucille Deroche wrote: Hi, My name is Lucille and I'm really new with Freesurfer : My questions are very basic, sorry. I just start a project in segmentation of cerebrum. For converting a surface in volume. I would like to use mri_surf2vol but for that I need a volume registration file . For creating that file, I would use autoreg-sess. In documentation, it is said that : 'The volume registration file contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume' My question is : what here, represent the anatomical reference ? The functionnal volume ? Secondly, for autoreg-sess, the arguments are the subject name and the subject directory. I think the registration I need to create must be between my 2 volumes, so should I use the subject name and subject directory for my 2 subjects ? Sorry,I am really messed... Cheers Lucille ___ 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] tracula FS 5.2
Hi Anastasia, I'm running tracula on linux ubuntu (mint 14) on a lenovo thinkpad edge. it has 8gb ram and 4 CPUs, i think it's a lot.. I did not run tracula before on this computer. Daria - Daria Antonenko, Dipl.-Psych. Charité - Universitätsmedizin Berlin NeuroCure Clinical Research Center NCRC AG Flöel Charitéplatz 1, 10117 Berlin Tel.: +49 30 450 560 223 Fax: +49 30 450 539 921 E-Mail: daria.antone...@charite.de -Ursprüngliche Nachricht- Von: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 10. April 2013 17:03 An: Antonenko, Daria Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] tracula FS 5.2 Hi Daria - How much memory does your system have? Were you ever able to run trac-all from the 5.1 version on the same system? a.y On Wed, 10 Apr 2013, Antonenko, Daria wrote: Hi FS experts, I tried to run Tracula with the new FS 5.2 release and came across memory allocation problems in the preprocessing step and would appreciate some advice on solving them: MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice Cannot allocate memory Linux daria-Think 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 i686 i686 i686 GNU/Linux trac-preproc exited with ERRORS at Tue Apr 9 22:21:43 CEST 2013 I attached the log-file. Let me know if you need further information about my system. Thank you in advance, Daria 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] Fwd: Comparing HRF undershoots between conditions
Yes, assuming a shape will give you much more power, at least for the individual subject. doug On 04/11/2013 02:55 AM, SHAHIN NASR wrote: Sorry that I keep on asking questions but I want to know if using a model can significantly increase the chance of getting a significant response. As far as I see for the positive peak, when I use a model (e.g. gamma model or spmhrf), I see a more significant response compared to when I use the FIR model. Is it correct? If true, then the same might be correct for the negative peak. P.S.: To be more clear, I am talking about the response maps relative to the baseline. On Apr 10, 2013 6:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: yes, that is what you want. The only other way that comes to mind is to model each event type as two event types one delayed relative to the other. Then model the responseto each as a gamma. If the delay is right, then the first gamma should model the main positive response and the second gamma will model the negative response. both will be independent from the other. doug On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu mailto:sha...@nmr.mgh.harvard.edu wrote: I think I figured it out but I want to double check. I am generating group-average map for my subjects using isxconcat-sess command which generates ces maps for each time frame. I think these maps are what I wanted. Right? If you still have other solutions that you think may generate more reliable results, I am eager to know. For instance, is there anyway to fit a model as we do for spmhrf or fslhrf, but just for the negative peak? Regards That's the problem Doug. I have already generated the FIR model but how can I show the sig MAP for one particulat time point. What are the other ways? On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.eduwrote: Hi Shahin, there are several ways that you could do it. The one that immediately comes to mind is to use an FIR and then test for a difference at a particular post stimulus time point. doug On 04/10/2013 03:54 PM, SHAHIN NASR wrote: Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak of activity) between two conditions independent from the positive peak. Is there anyway, to generate this map? P.S.: Please note that I need a map and not a time course graph. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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
Re: [Freesurfer] mri_aparc2aseg issue
Hi Paul, try using this color table, something like tkmedit HS_001 orig.mgz -seg aug_aparc+aseg.mgz paul.ctab doug On 04/08/2013 10:02 AM, Paul Beach wrote: Hi Freesurfers, I'm currently trying to take manually made ROIs (label files) that have been incorporated into new annotation files (one for each hemisphere - rh.aug_aparc.annot lh.aug_aparc.annot) and turn them into a new (augmented) annotation into a aseg file (an aug_aparc+aseg.mgz file). To do so I've been using the mri_aparc2aseg command and, at face value, it works well. However, some of my ROIs (specifically my insular ROIs) are being either shifted or lost in the transition from annotation to segmentation. Note that each hemisphere's new annotation files look perfect on tksurfer (which is where they were originally drawn). It's only when I try and make them fill the full cortical ribbon with the mri_aparc2aseg command that I get this issue. I piloted everything out on averaged subject and it all worked perfectly. However, when I attempted things on individual subject data I received the problem described above. I've attached a picture illustrating the discrepancy between the an averaged subject and a single subject. I have also attached my script code. The overall goal is to create a gmroi_volume which will allow me to determine an aux number of each manual ROI so as to export each one to AFNI space. I'd *really* appreciate help on how to fix this. Thanks, Paul ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 0 Unknown 0 0 0 0 1 Left-Cerebral-Exterior 70 130 180 0 2 Left-Cerebral-White-Matter 245 245 245 0 3 Left-Cerebral-Cortex205 62 78 0 4 Left-Lateral-Ventricle 120 18 134 0 5 Left-Inf-Lat-Vent 196 58 250 0 6 Left-Cerebellum-Exterior0 148 0 0 7 Left-Cerebellum-White-Matter220 248 164 0 8 Left-Cerebellum-Cortex 230 148 34 0 9 Left-Thalamus 0 118 14 0 10 Left-Thalamus-Proper0 118 14 0 11 Left-Caudate122 186 220 0 12 Left-Putamen236 13 176 0 13 Left-Pallidum 12 48 255 0 14 3rd-Ventricle 204 182 142 0 15 4th-Ventricle 42 204 164 0 16 Brain-Stem 119 159 176 0 17 Left-Hippocampus220 216 20 0 18 Left-Amygdala 103 255 255 0 19 Left-Insula 80 196 98 0 20 Left-Operculum 60 58 210 0 21 Line-1 60 58 210 0 22 Line-2 60 58 210 0 23 Line-3 60 58 210 0 24 CSF 60 60 60 0 25 Left-Lesion 255 165 0 0 26 Left-Accumbens-area 255 165 0 0 27 Left-Substancia-Nigra 0 255 127 0 28 Left-VentralDC 165 42 42 0 29 Left-undetermined 135 206 235 0 30 Left-vessel 160 32 240 0 31 Left-choroid-plexus 0 200 200 0 32 Left-F3orb 100 50 100 0 33 Left-lOg135 50 74 0 34 Left-aOg122 135 50 0 35 Left-mOg51 50 135 0 36 Left-pOg74 155 60 0 37 Left-Stellate 120 62 43 0 38 Left-Porg 74 155 60 0 39 Left-Aorg 122 135 50 0 40 Right-Cerebral-Exterior 70 130 180 0 41 Right-Cerebral-White-Matter 0 225 0 0 42 Right-Cerebral-Cortex 205 62 78 0 43 Right-Lateral-Ventricle 120 18 134 0 44 Right-Inf-Lat-Vent 196 58 250 0 45 Right-Cerebellum-Exterior 0 148 0 0 46 Right-Cerebellum-White-Matter 220 248 164 0 47 Right-Cerebellum-Cortex 230 148 34 0 48 Right-Thalamus 0 118 14 0 49 Right-Thalamus-Proper 0 118 14 0 50 Right-Caudate 122 186 220 0 51 Right-Putamen 236 13 176 0 52 Right-Pallidum
[Freesurfer] LME and clusterwise correction
Hi, I am doing a longitudinal analysis using the LME toolbox, and I would like to perform a clusterwise correction for multiple comparisons. Would it be correct to use mri_surfcluster on the resulting maps, or do you suggest any alternative otherwise ? I can only find functions implementing FDR correction in the toolbox. Thanks, Benjamin -- Benjamín Garzón, Ph.D. Karolinska Institutet Department of Neuroscience Retzius Väg 8 17177 Stockholm (SWEDEN) ___ 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] Autoreg-sess and mri_surf2vol
Hi Lucile, don't use autoreg-sess (that is an old program and was for fMRI). Use mri_surf2vol with --identity subjectname instead of --reg doug On 04/11/2013 11:45 AM, Lucille Deroche wrote: Hi Bruce, In fact, have 2 differents surfaces of pial surface. I would like to save my surfaces in volume to be able to calculate the dice score between the two. Cheers Lucille *De :* Bruce Fischl fis...@nmr.mgh.harvard.edu *À :* Lucille Deroche lucilledero...@yahoo.fr *Cc :* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Envoyé le :* Jeudi 11 avril 2013 11h18 *Objet :* Re: [Freesurfer] Autoreg-sess and mri_surf2vol Hi Lucille what do you mean by converting a surface to the volume? What do you want to do with it? What volume would you like to convert it to? cheers Bruce On Thu, 11 Apr 2013, Lucille Deroche wrote: Hi, My name is Lucille and I'm really new with Freesurfer : My questions are very basic, sorry. I just start a project in segmentation of cerebrum. For converting a surface in volume. I would like to use mri_surf2vol but for that I need a volume registration file . For creating that file, I would use autoreg-sess. In documentation, it is said that : 'The volume registration file contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume' My question is : what here, represent the anatomical reference ? The functionnal volume ? Secondly, for autoreg-sess, the arguments are the subject name and the subject directory. I think the registration I need to create must be between my 2 volumes, so should I use the subject name and subject directory for my 2 subjects ? Sorry,I am really messed... Cheers Lucille ___ 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: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
Re: [Freesurfer] DTI: problems with (high) FA values
That is a good value, so the regis not the problem. If you upload your dt_recon folder as well as your recon-all folder for that subject I'll take a look. doug On 04/11/2013 10:02 AM, Rotem Saar wrote: Hi Douge, In your last reply to my email (that contained questions regarding some really high FA values - see recent emails below), u asked me to write u the first value in register.dat.mincost - I'm copying the line I have: 0.280554 140.210312 156.795241 11.152485 Does this takes us one step further towards understanding the problem and its solution ? Thanks for your time, Rotem On 04/07/2013 06:48 AM, Rotem Saar wrote: Hi Doug, Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ? *_yes, the ventricles look too high_* When I first run the script, I got all values and looked the the CC - it looked fine. Then, I wanted to validate with some other regions, just to show that I got the appropriate (low) FA values for regions I don't expect to see high values in - and things looked odd (too high). I remember Bruce also writing me that the values seems a little high, but we didn't further discuss. I read the following this link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual The CC has an average FA of about 0.75, gyral parcellations are about 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as expected because the CC is highly directional with no crossing fibers so we would expect the CC to have the highest FA. The gyral white matter is also directional but has fibers crossing in them, so one expects the FA to be lower than CC. The gray matter (putamen) is still lower. The ventricle has no fibers, so we expect it to have the lowest FA. All my values are above 0.4 Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/ subjects/Rotem_try/mri/wmparc.mgz why do I get 182 regions ? in my wmparc.stats I have only 70... The wmparc includes all the subcortical and cortical regions too, but only the WM regions are reported in the wmparc.stats file. *_To only report the WM regions, add to mri_segstats --ctab $FREESURFER_HOME/_**_WMParcStatsLUT.txt_* I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help. _*I don't know either. If I had to guess, I'd say it is a registration problem. What is the first value in register.dat.mincost?*_ doug Attached is the table again, Thanks Rotem The values look about right in the table. Your pipeline looks ok, thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output of mri_vol2vol (fa_FOLDER-NAME.nii). doug On 03/17/2013 02:16 AM, Rotem Saar wrote: Hi all, I run into somthing that seems odd to me and wanted to consult - I run the following script for getting the FA values from my DTI scans: 1) dt_recon --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I1.dcm --s FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec 2) tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii -fthresh 0.2 -fmax 1 4) mri_vol2vol --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s FOLDER-NAME --interp nearest --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat 5) tkregister2 --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg 6) mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii --sum /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME I got a table with all the FA values (see attached),
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Hi PPJ and all, I found that the 5.2 – 5.1 difference is primarily seen in the cortical thickness, and much less so in the aseg.volume. Here, I picked right-amygdala volume as an example of aseg.volume and rh_bankssts_thickness as an example of rh.aparc.thickness. While the correlation between the two versions of right-amygdala is r = .92 (n = 161), that of the rh_bankssts_thickness is r = .45. Presumably I believe the correlation should be .90 for a strong continuity between the two versions? Do you have anything in the cortical thickness? Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 From: Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.brmailto:p...@netfilter.com.br Date: Wednesday, April 10, 2013 11:07 AM To: Daniel Yang yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu Cc: Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 Ok, I'll try to put together a stat from aparc too. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.brhttp://www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 12:04 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Hi PPJ, Thanks! It looks interesting. I also found FS 5.2 is faster. Is there any chance you could also provide the cortical thickness of the 2009 atlas (e.g., rh)? I will take a look into the aseg.volume in my data too. Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454tel:%28203%29%20737-5454 From: Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.brmailto:p...@netfilter.com.br Date: Wednesday, April 10, 2013 10:49 AM To: Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu Cc: Daniel Yang yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu, freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 You'll find attached some preliminary data of the comparison we did among versions. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.brhttp://www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi PPJ That's exactly what we are doing. Good to hear its stable for you Bruce On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira Juniorp...@netfilter.com.brmailto:p...@netfilter.com.br wrote: I have processed more that 600 brains with both versions in the last weeks and the only difference I'm seeing between version 5.2.0 and 5.1, besides the obvious new features, is processing time. Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance. Besides that there's no visible difference in terms of cortical thickness, volumes, etc. If you have access to computer resources to spare you can run recon-all of both versions in some well known database of images and do a more formal test. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.brhttp://www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454tel:%28203%29%20737-5454 On 3/19/13 7:07 AM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Posting one of the brains. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn It seems to me that neither version is perfect; however, 5.2.0 is capturing more black spaces in the region I'm looking at. It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20).
[Freesurfer] Fwd: Sample size estimation from LME models
Hi,
I am new to Freesurfer and the Linear Mixed Effects (LME) Models packages.
And I would like to compute sample size from volumetric measures for 2
groups.
I followed the longitudinal example provided in the wiki (
http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#a.29Univariate),
with the ADNI example. But I am not sure what to use for the common random
effect design matrix Zi and column ZiCol with the
lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,dr,pw,alpha,gr_pr)
function:
Here is what I do in matlab:
load('ADNI791_Hipp_and_Entorh.mat')
total_hipp_vol_stats = lme_fit_EM(X_Hipp,[1,2],Y(:,1)+Y(:,2),ni);
lme_plannedSampleSize(total_hipp_vol_stats.X,[1,2]
,total_hipp_vol_stats.Dhat,total_hipp_vol_stats.phisqhat,1,.2,.8,0.05)
ans =
1.0e+07 *
1.35840.0154
0.01540.0100
Is that right?
Regards,
Nicolas
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Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Thanks Nick! I have uploaded the relevant files to you. Thanks, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 4/10/13 1:19 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Daniel, We're repeating our paired-analysis of thickness measures between 5.1 and 5.2. In the meantime, to check for correctness, open the brain.finalsurfs.mgz file with the surfaces overlayed, and check the intensity value of the voxels which appear to be non-cortical 'black spaces', relative to neighboring gm voxels. ignore the aseg.mgz gm voxels, as those are not accurate (ie, dont load aseg.mgz when inspecting surfaces, or at least turn if off when inspecting gm regionsits still handy to see where hippocampus sits). Nick On Wed, 2013-04-10 at 11:11 +, Yang, Daniel wrote: Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel 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] Autoreg-sess and mri_surf2vol
Try: mri_surf2vol --surf pial --mkmask --hemi lh --identity subjid --template subjid/mri/norm.mgz --o subjid/mri/pial_in_vol.mgz FWIW, I'm not sure if sampling two surfaces to the volume, and then computing a dice coefficient is really the best way to compare two surfaces. I would instead compare the two surfaces directly -- e.g., the rms distance between matched vertices. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Lucille Deroche lucilledero...@yahoo.fr Reply-To: Lucille Deroche lucilledero...@yahoo.fr Date: Thursday, April 11, 2013 2:39 PM To: Doug Greve gr...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Autoreg-sess and mri_surf2vol Hi, I did the command: mri_surf2vol --surfval $SUBJECTS_DIR/Patient1/surf/rh.pial --hemi rh --identity Patient1. ERROR: cannot recognize the type of /home/lucille/Freesurfer/freesurfer/subjects/Patient1/surf/rh.pial The name of my subject is ' Patient1'. Did I do a wrong entery at the --surfval argument ? Cheers Lucille De : Douglas N Greve gr...@nmr.mgh.harvard.edu À : freesurfer@nmr.mgh.harvard.edu Envoyé le : Jeudi 11 avril 2013 12h49 Objet : Re: [Freesurfer] Autoreg-sess and mri_surf2vol Hi Lucile, don't use autoreg-sess (that is an old program and was for fMRI). Use mri_surf2vol with --identity subjectname instead of --reg doug On 04/11/2013 11:45 AM, Lucille Deroche wrote: Hi Bruce, In fact, have 2 differents surfaces of pial surface. I would like to save my surfaces in volume to be able to calculate the dice score between the two. Cheers Lucille *De :* Bruce Fischl fis...@nmr.mgh.harvard.edu *À :* Lucille Deroche lucilledero...@yahoo.fr *Cc :* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Envoyé le :* Jeudi 11 avril 2013 11h18 *Objet :* Re: [Freesurfer] Autoreg-sess and mri_surf2vol Hi Lucille what do you mean by converting a surface to the volume? What do you want to do with it? What volume would you like to convert it to? cheers Bruce On Thu, 11 Apr 2013, Lucille Deroche wrote: Hi, My name is Lucille and I'm really new with Freesurfer : My questions are very basic, sorry. I just start a project in segmentation of cerebrum. For converting a surface in volume. I would like to use mri_surf2vol but for that I need a volume registration file . For creating that file, I would use autoreg-sess. In documentation, it is said that : 'The volume registration file contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume' My question is : what here, represent the anatomical reference ? The functionnal volume ? Secondly, for autoreg-sess, the arguments are the subject name and the subject directory. I think the registration I need to create must be between my 2 volumes, so should I use the subject name and subject directory for my 2 subjects ? Sorry,I am really messed... Cheers Lucille ___ 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: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
Re: [Freesurfer] merging dti data
Hi Doug I can motion correct the briks with 3dvolreg 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: Thursday, April 11, 2013 11:22:13 AM Subject: Re: [Freesurfer] merging dti data That might work. I think motion correction is going to be your biggest problem since the slabs were acquired at different times. On 04/11/2013 11:05 AM, Jon Wieser wrote: the gradients were the same for each slab. What is the difficulty with runnning the merged brain halves in tracula? I have another to do it that I am going to try. I made AFNI Brik's of the two slabs, and merged them together into one AFNI brik with the AFNI command 3dZcat. I made a nifti file from the merged afni brik. i will try running tracula on the merged nifti file. Jon - Original Message - From: Douglas Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, April 11, 2013 9:56:53 AM Subject: Re: [Freesurfer] merging dti data yes, they work for whole brain, but not if you have two brain halves. You might be able to do something in matlab. I assume the gradient direction order was the same for both slabs? doug On 4/11/13 10:36 AM, Jon Wieser wrote: Those commands were given to me by Anastasia. they work fine for merging two whole brain datasets. jon - Original Message - From: Douglas Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 10, 2013 10:13:05 PM Subject: Re: [Freesurfer] merging dti data Hi Jon, I don't know how to make this work, but I'm sure that those commands will not do it. Sorry:( doug On 4/10/13 1:13 PM, Jon Wieser wrote: we captured some dti data. there were 2 runs. we acquired in the axial plane, 2mm slice thickness the first run captured the lower half of the brain, slice locations: I56-S20, and the second run captured the upper half of the brain S16-S92. i have made briks from each of these runs. I can convert the briks to nifti files I want to merge the nifti files together to analyze the data in tracula In the past i have merged data from two dti runs, but each run have covered the entire brain, with the following commands mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz would it work to concat the two half brain niftis into one file and analyze that with tracula? (I will concat the bvec and bvals files too) would this cause problems doing it this way? Thanks Jon ___ 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. -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Autoreg-sess and mri_surf2vol
yes, I agree. Two surfaces could be extremely close and have 0 dice. I don't think it would be as informative as Hausdorff or RMS as Mike suggests Bruce On Thu, 11 Apr 2013, Michael Harms wrote: Try: mri_surf2vol --surf pial --mkmask --hemi lh --identity subjid --template subjid/mri/norm.mgz --o subjid/mri/pial_in_vol.mgz FWIW, I'm not sure if sampling two surfaces to the volume, and then computing a dice coefficient is really the best way to compare two surfaces. I would instead compare the two surfaces directly -- e.g., the rms distance between matched vertices. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Lucille Deroche lucilledero...@yahoo.fr Reply-To: Lucille Deroche lucilledero...@yahoo.fr Date: Thursday, April 11, 2013 2:39 PM To: Doug Greve gr...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Autoreg-sess and mri_surf2vol Hi, I did the command: mri_surf2vol --surfval $SUBJECTS_DIR/Patient1/surf/rh.pial --hemi rh --identity Patient1. ERROR: cannot recognize the type of /home/lucille/Freesurfer/freesurfer/subjects/Patient1/surf/rh.pial The name of my subject is ' Patient1'. Did I do a wrong entery at the --surfval argument ? Cheers Lucille _ De : Douglas N Greve gr...@nmr.mgh.harvard.edu À : freesurfer@nmr.mgh.harvard.edu Envoyé le : Jeudi 11 avril 2013 12h49 Objet : Re: [Freesurfer] Autoreg-sess and mri_surf2vol Hi Lucile, don't use autoreg-sess (that is an old program and was for fMRI). Use mri_surf2vol with --identity subjectname instead of --reg doug On 04/11/2013 11:45 AM, Lucille Deroche wrote: Hi Bruce, In fact, have 2 differents surfaces of pial surface. I would like to save my surfaces in volume to be able to calculate the dice score between the two. Cheers Lucille *De :* Bruce Fischl fis...@nmr.mgh.harvard.edu *À :* Lucille Deroche lucilledero...@yahoo.fr *Cc :* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Envoyé le :* Jeudi 11 avril 2013 11h18 *Objet :* Re: [Freesurfer] Autoreg-sess and mri_surf2vol Hi Lucille what do you mean by converting a surface to the volume? What do you want to do with it? What volume would you like to convert it to? cheers Bruce On Thu, 11 Apr 2013, Lucille Deroche wrote: Hi, My name is Lucille and I'm really new with Freesurfer : My questions are very basic, sorry. I just start a project in segmentation of cerebrum. For converting a surface in volume. I would like to use mri_surf2vol but for that I need a volume registration file . For creating that file, I would use autoreg-sess. In documentation, it is said that : 'The volume registration file contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume' My question is : what here, represent the anatomical reference ? The functionnal volume ? Secondly, for autoreg-sess, the arguments are the subject name and the subject directory. I think the registration I need to create must be between my 2 volumes, so should I use the subject name and subject directory for my 2 subjects ? Sorry,I am really messed... Cheers Lucille ___ 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: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
Re: [Freesurfer] final skull-stripped file?
Hi Marco, the aparc+aseg.mgz is probably going to be the best one (it is what I use:). When you binarize it, you can dilate it by a voxel as well with: mri_binarize --i aparc+aseg.mgz --min 0.5 --dilate 1 --o yourmask.mgz doug On 04/11/2013 03:31 PM, Marco Loggia, PhD wrote: Dear all, what is the 'best' skull stripped file produced by freesurfer? From what I see, it would seem to be 'brainmask'. However this file -if I understand correctly- is produced in the very first stages of recon-all, and therefore does not take advantage of the detailed reconstruction of the brain 'borders' which is achieved in the subsequent stages of recon-all. For this reason, I have been masking my brainmask.mgz file with a binary file created using the aparc+aseg file (which labels only the brain), slightly smoothed to be conservative in the stripping. Or is there already a file skull-stripped this way? Thanks, Marco __ Marco L. Loggia, PhD Instructor in Radiology Harvard Medical School Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 ma...@nmr.mgh.harvard.edu mailto:ma...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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] Fwd: Sample size estimation from LME models
Hi Nicolas
The common random effects design matrix expression
means that all subjects in your prospective study are expected in
advance to have the same random effects design matrix (Zi). If you
assume a linear trajectory over time and a two-year study with repeated
measurements every six months then this matrix can be:
1 0
1 0.5
1 1
1 1.5
1 2
In this case you are considering both intercept and time as random effects.
ZiCol
is the column of the above matrix that you are interested in (usually column 2,
slope of change over time).
To
compute sample size you also need estimates of the random effects
covariance matrix (Dhat), within-subject measurement error, effect size,
and drop-out rate. If your study is about Alzheimer-related hippocampal
volume or cortical thickness variations you can use our sample ADNI
data to compute those values (ADNI791_Hipp_and_Entorh.mat). Eg.
lme_plannedSampleSize(Zi,2,total_hipp_vol_stats.Dhat,total_hipp_vol_stats.phisqhat,1,.2,.8,0.05)
Alternatively,
you can perform a pilot longitudinal study with a small sample or you
can use information from previous studies that are similar to the study
that you are planning to run, or you can even analyse some public
available longitudinal data with lme to compute those values.
We performed sample size estimations for the study described in our paper in
the wiki page:
http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
It may be useful for you to take a look at it.
Best
-Jorge
De: nicolas guizard n.guiz...@gmail.com
Para: freesurfer@nmr.mgh.harvard.edu
Enviado: Jueves 11 de abril de 2013 14:28
Asunto: [Freesurfer] Fwd: Sample size estimation from LME models
Hi,
I am new to Freesurfer and the Linear Mixed Effects (LME) Models packages. And
I would like to compute sample size from volumetric measures for 2 groups.
I followed the longitudinal example provided in the wiki
(http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#a.29Univariate),
with the ADNI example. But I am not sure what to use for the common random
effect design matrix Zi and column ZiCol with the
lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,dr,pw,alpha,gr_pr) function:
Here is what I do in matlab:
load('ADNI791_Hipp_and_Entorh.mat')
total_hipp_vol_stats = lme_fit_EM(X_Hipp,[1,2],Y(:,1)+Y(:,2),ni);
lme_plannedSampleSize(total_hipp_vol_stats.X,[1,2],total_hipp_vol_stats.Dhat,total_hipp_vol_stats.phisqhat,1,.2,.8,0.05)
ans =
1.0e+07 *
1.3584 0.0154
0.0154 0.0100
Is that right?
Regards,
Nicolas
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Re: [Freesurfer] bblabel values for DLPFC
Dear Doug, I used bblabel for making coronal cut. The definition is given below. bblabel Applies a bounding box to a label. The bounding box is specified by six coordinates (xmin,xmax,ymin,ymax,zmin,zmax). Only those label points within this box are copied to the output. If a min is not specified, then -infinity is used. If a max is not specified, then +infinity is used. Example: bblabel --l lh.G_cuneus.label --o lh.out.label --xmin 0 --ymax -90 --zmin 10 --zmax 20 Keeps label points from lh.G_cuneus.label that have x 0, y -90, and z between 10 and 20. The result is stored in lh.out.label. So I suppose, there would be X, Y, Z values for DLPFC region also.It's ok, if you don't know much about it. Thanks for your support. From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 10, 2013 12:22 AM Subject: Re: [Freesurfer] bblabel values for DLPFC I don't know that there is such a definition of DLPFC. doug On 04/09/2013 04:52 AM, Anupa AV wrote: Dear All, I 'd like to know the xmin, ymin and zmin for creating DLPFC label using bblabel string. I want to make a coronal cut at y=26 for seperating DLPFC from premotor cortex. I tried by giving a value of xmin=0, ymin=26 and zmin= 0. I'd like to know whether I'm on right track. Thanks in advance for your response. ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.___ Freesurfer 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.
