Freesurfer

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30089 discussions

Re: [Freesurfer] Non-rigid registration approaches
by Hedyeh Javaheri 25 Apr '18

25 Apr '18

External Email - Use Caution Hi Douglas, I applied a non-rigid registration to my nifti files using another software (IRTK) and then tried to run dt_recon in Freesurfer. Dt_recon is failing during Fitting Tensors and the error message it is displaying is "ERROR: DTIstructFromBFiles(): dimension mismatch" the error message goes on to say that my bvecs file has 99 rows while my bvals file has 11 rows. I've looked at my bvecs and bvals files: the bvecs has 33 rows and 3 columns, and the bvals has 33 rows and 1 column. Can you tell me what the problem is? Is there a way to get past this error? -Hedyeh Date: Tue, 24 Apr 2018 13:20:20 -0400 From: Douglas Greve <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Non-rigid registration approaches To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <52506cd6-286b-21a0-859a-1cda85557bad(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Sorry, I don' know what to tell you. On 4/21/18 5:34 PM, Hedyeh Javaheri wrote: > > > Thanks for your reply Douglas, > > I am trying co-register the Diffusion data onto the original > structural MRIs. I have tried bbregister and mri_vol2vol but the > results are not great. I realized that the diffusion data have a lot > of distortions, so the rigid and/or affine co-registration is not > sufficient. Do you recommend performing a non-rigid registration in > this case? If you do, do you know of any ways to do that within > Freesurfer? > > > Thanks > > -Hedyeh

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Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found
by Nillo, Ryan Michael R 25 Apr '18

25 Apr '18

External Email - Use Caution Hello FreeSurfer users, I am trying to run hippocampal subfield segmentation on our subjects on FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an error relatively early: /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin//kvlAutoCrop: line 3: kvlAutoCrop.bin: command not found When I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin, kvlAutoCrop.bin was located there, as expected. When I tried to run the step manually, it produced the correct output, but the next step gave me the similar error: command not found. I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin and saw all the other binaries were there, as well. The binaries are correctly exported on my PATH. I also made sure to download the Matlab compiler runtime and made sure they were on my PATH. I am running freesurfer on a Linux machine with the RedHat 7.5 OS.Any help is greatly appreciated. Thanks, Ryan

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Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found
by Nillo, Ryan Michael R 25 Apr '18

25 Apr '18

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Arcuate fasciculus seed regions in MNI space
by Juergen Haenggi 25 Apr '18

25 Apr '18

External Email - Use Caution Dear tractography experts does anyone have the arcuate fasciculus seed regions in MNI space and is willing to share these seeds with us? we are also interested in MNI space seed regions of the different parts of the SLF (according work done by Catani and colleagues). Thanks in advance Regards Jürgen ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This email (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this email in error) please notify the sender immediately and destroy this email. Any unauthorised copying, disclosure or distribution of the material in this email is strictly forbidden. -----------------------------------------------------------------------------------------------------

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Segmentation issue with FS6
by Barlow, Cody 24 Apr '18

24 Apr '18

External Email - Use Caution Hi FreeSurfer Experts, After running my subject through FS6 autorecon3 and QCing the data, I noticed that FS6 is outlining white matter as grey matter and then bumping out the grey matter segmentation accordingly. I have tried using different watershed preflood heights during various skull strips with no success as well as using the flag gcut. I'm thinking the issue has to do with atrophy due to my subject population, dementia patients, or poor contrast between GM and WM during image acquisition. Is there a flag or tkmedit tool I can use to help solve this problem. I have attached an image showing the issue. Thanks for the help, Cody

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Calculation of surface area
by Zohar Berman 24 Apr '18

24 Apr '18

External Email - Use Caution Dear FreeSurfer experts, Can one use the volume and cortical thickness of a region to calculate the surface area of this region? Thanks a lot in advance! Best, Zoi

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Recon-all w/ Hammersmith atlas
by Ryan Flores 24 Apr '18

24 Apr '18

Hi Freesurfer Developers, Our group is hoping to obtain the cortical thickness, surface area, and volume for various cortical regions (as well as some subcortical volumes); however, we would like these values to be outputted with respect to the regions delineated in the Hammersmith atlas. This atlas is available for free online (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-…) and I’ve included a screenshot to show you what files are included in the download. Based on this information, what is the best and/or most straight forward to move forward? Thank you for your time. I look forward to hearing from you. 1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 2. Platform: macOS High Sierra (Version 10.13.1) Best, Ryan -- Ryan Flores Clinical Research Coordinator

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resting state motion censoring
by Adam Martersteck 24 Apr '18

24 Apr '18

Hi Freesurer experts, I’m looking to censor (drop volumes) from my resting state fMRI time series that violate a predetermined motion and signal threshold (FD and DVARS). I've already determined which volumes violate X and Y criteria. Is there a way to to tell FS to "ignore" these time points in the analysis such as in preproc-sess or mkanalysis-sess? If there is not and if I were to drop the volumes directly from the 4D file before starting any pre-processing and analysis – would that be a problem for finding and regressing the auto-correlation in the time series? Thanks! Adam

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Re: [Freesurfer] Non-rigid registration approaches
by Hedyeh Javaheri 24 Apr '18

24 Apr '18

External Email - Use Caution Thanks for your reply Douglas, I am trying co-register the Diffusion data onto the original structural MRIs. I have tried bbregister and mri_vol2vol but the results are not great. I realized that the diffusion data have a lot of distortions, so the rigid and/or affine co-registration is not sufficient. Do you recommend performing a non-rigid registration in this case? If you do, do you know of any ways to do that within Freesurfer? Thanks -Hedyeh ------------------------------------------------------------ ----------------------------------------------------------------- Date: Tue, 17 Apr 2018 11:49:04 -0400 From: Douglas Greve <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Non-rigid registration approaches To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <763da2ef-359a-9f44-9b54-1f96acb3b2ef(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Not really. Are you trying to account for B0 distortion in the DTI? If you have a B0 map, you can pass that to bbregsiter and mri_vol2vol to account for it On 4/16/18 10:29 AM, Hedyeh Javaheri wrote: > Hello all, > > I am performing DTI analysis and wanted to know if Freesurfer has a > tool for non-rigid registration. > I performed recon-all and dt_recon on my subject and then used the > register.dat file that was generated by dt_recon to convert the > dt_recon output files back into the space of my orig.nii file from the > recon-all output. Now I need to register the files in the orig.nii > space back onto the T1 MRI that is in native space. > > I have tried using? mri_vol2vol to get the files in the orig.nii > (recon-all) space into the T1 native space without using a > registration file (I used --regheader) and now the registration matrix > of my file is the same as the native space, but when I use rview to > visualize the registration there are flaws. I've also tried this > co-registration using tkregister2 to create a registration file called > register.native.dat, and then used mri_vol2vol with > register.native.dat; and the results were the same as when I used > mri_vol2vol with --regheader. > > Is there a tool to do actual manual registration in Freesurfer? Using > tkregister2 I cannot perform localized changes; and the global changes > it is capable of do not improve on the coregistration. > > Here is a breakdown of what I have done: > > subject in Native space to Freesurfer conformed space using recon-all, > output: orig.nii > subject in Native space to other Freesurfer space using dt_recon, > output: lowb.nii and register.dat > From the other Freesufer space to Freesurfer conformed space using > register.dat, output: lowb2orig.nii > attempting to convert from Freesurfer conformed space to Native space: > ? ? ? ? ? ? ? ? ? using mri_vol2vol and --regheader --> poor registration > ? ? ? ? ? ? ? ? ? using tkregister2 to make register.native.dat, then > mri_vol2vol and ?register.native.dat --> poor registration > > I am running Freesurfer version 6 on Windows. > > Thanks in advance! > -Hedyeh Javaheri

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Re: [Freesurfer] mri_vol2surf: unable to compare volume maps
by Douglas Greve 24 Apr '18

24 Apr '18

please remember to post to the list ... Run tkregister --mov negative_allsocial_proportion.nii --regheader --reg deleteme.lta --s collin --surfs where collin is the name of the subject you gave when you analyzed the collin brain in recon-all. If this looks like it is in register, then using --regheader with mri_vol2surf should work. If it is not, then tkregister --mov negative_allsocial_proportion.nii --identity --reg identity.lta --s collin --surfs If that looks ok, then save the registration and use that when running mri_vol2surf On 4/20/18 3:48 PM, srishti goel wrote: > > External Email - Use Caution > > Hi Douglas, > > Following up on where I left, our maps > (negative_allsocial_proportion.nii) were created using *neuroelf > *software and can be viewed in neuroelf on the *Colins template* > (colin_brain_ICBMnorm.vmr). I exported this template as a nifti file > and did recon-all for this file but I am still stuck with the same > issue. I can run mri_vol2surf on our maps using the colins template > but then how do I compare the maps that I am trying to compare because > the other map in on the surface of MNI template in FS. I want to be > able to produce the two maps on the same surface. > > Please let me know if you have thoughts about it. > > Thanks so much! > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srishtig(a)email.unc.edu <mailto:srishtig@email.unc.edu> > skype: srishti.goel12 > > > On Thu, Apr 12, 2018 at 10:51 AM, Douglas N. Greve > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: > > Hi Srishti, you will need to be much more specific to allow me to > help you. mni152_subject is not a file that can be input to > recon-all (it should be a dicom or nifti or mgz). If you use the > same input to recon-all that you used to view it in spm, then the > FS output should align with your map. > > > On 04/12/2018 10:41 AM, srishti goel wrote: > > mni152_subject is the file that has been used for recon-all. > Our collaborators had run recon-all with that file so we did > not do it again. As far as the 'MNI template' is concerned, I > didn't do that part of the analysis so I am unsure which > specific file it is, but it MNI 152. > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > skype: srishti.goel12 > > > On Thu, Apr 12, 2018 at 10:28 AM, Douglas N. Greve > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>> wrote: > > What is the "MNI template" that you are using. I mean an > exact file > used. Did you use this file when you ran recon-all? > > > On 04/12/2018 10:23 AM, srishti goel wrote: > > Yeah, I am unsure where to go from here as well. So the > results > can be > > viewed in SPM and on the MNI template space itself, > since SPM > > typically does not have a problem showing multiple images in > different > > sizes. > > > > Best, > > Srishti > > Social/Clinical Research Specialist > > Child Imaging Research and Life Experiences Lab > > University of North Carolina at Chapel Hill > > email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>> > > skype: srishti.goel12 > > > > > > On Thu, Apr 12, 2018 at 10:11 AM, Douglas N. Greve > > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>> > wrote: > > > > When you use bbregister, it is expecting the input > nii file to > > represent > > the actual anatomy of the subject, so it does not > surprise > me that it > > does not work that well. I'm not sure what to do > about this > because a > > meta analysis image will never have decent anatomy. In > theory, it > > should > > be already in alignment with the mni152, but this is > trickier than it > > seems. How do you usually view the results? In FSL > or SPM? > Do you view > > them on an anatomical image? > > > > > > On 04/12/2018 09:03 AM, srishti goel wrote: > > > Hi Douglas, > > > > > > The negative_allsocial_proportion.nii file has > actually been > > converted > > > from a vmp file - 'negative_allsocial.vmp'. We used > neruoelf to > > > convert the vmp file, option - 'export to analze' and > 'export to > > > nifti'. The original vmp file represent the > results of a > > meta-analysis. > > > > > > Let me know if that helps or you would need more > information. > > > > > > Thanks! > > > > > > Best, > > > Srishti > > > > > > Best, > > > Srishti > > > Social/Clinical Research Specialist > > > Child Imaging Research and Life Experiences Lab > > > University of North Carolina at Chapel Hill > > > email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>> > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>>> > > > > skype: srishti.goel12 > > > > > > > > > On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve > > > <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>>> > > wrote: > > > > > > how was negative_allsocial_proportion.nii created? > > > > > > > > > On 4/11/18 9:14 PM, srishti goel wrote: > > >> Hi, > > >> > > >> I used bbregister to register: > > >> bbregister --mov > negative_allsocial_proportion.nii --s > > >> mni152_subject --bold --lta register.lta > > >> and then viewed it using: > > >> tkregisterfv --mov > negative_allsocial_proportion.nii > --reg > > >> register.lta --surfs > > >> It doesn't look great but it still looks okay > (Screenshot > > attached). > > >> Then I also used lta in tkregisterfv, as: > > >> tkregisterfv --mov > negative_allsocial_proportion.nii > --reg > > >> register.lta --s mni152_subject --surfs --reg > reg.deleteme.dat > > >> In this file, the volume map still lies > outside the > surface. > > >> Could you please help me resolve this issue. > > >> I tried using register.lta file in the > mri_vol2surf > but the > > >> overlay map doesn't show up again. > > >> Thanks! > > >> > > >> Best, > > >> Srishti > > >> Social/Clinical Research Specialist > > >> Child Imaging Research and Life Experiences Lab > > >> University of North Carolina at Chapel Hill > > >> email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>> > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>>> > > >> skype: srishti.goel12 > > >> > > >> > > >> On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve > > >> <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>>> > > wrote: > > >> > > >> don't use --init-rr ( you don't need to > spec an > init in > > >> version 6) > > >> > > >> > > >> On 4/10/18 9:48 PM, srishti goel wrote: > > >>> When I run bbregister, it gives me an error. > Attached > > is the > > >>> register.dat.log file for it. > > >>> Error: > > >>> > > >>> reading source > './tmp.bbregister.91068/template.nii'... > > >>> > > >>> mri_robust_register.bin: only pass single frame > MRI source > > >>> ./tmp.bbregister.91068/template.nii. > > >>> > > >>> > > >>> No such file or directory > > >>> > > >>> > > >>> Any help is greatly appreciated! > > >>> > > >>> > > >>> Best, > > >>> Srishti > > >>> Social/Clinical Research Specialist > > >>> Child Imaging Research and Life > Experiences Lab > > >>> University of North Carolina at Chapel Hill > > >>> email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>> > > >>> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>>> > > >>> skype: srishti.goel12 > > >>> > > >>> > > >>> On Tue, Apr 10, 2018 at 11:07 AM, > Douglas Greve > > >>> <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>>> > > wrote: > > >>> > > >>> They are not in registration. Try > running > > bbregister to > > >>> create a registration file (lta), > then pass > the lta to > > >>> tkregisterfv instead of --regheader > > >>> > > >>> > > >>> On 4/9/18 11:49 PM, Bruce Fischl wrote: > > >>>> How did you generate the > registration? And give > > us the > > >>>> details of what you are trying to > register > > >>>> Cheers > > >>>> Bruce > > >>>> > > >>>> On Apr 8, 2018, at 2:55 PM, srishti > goel > > >>>> <23srishtigoel(a)gmail.com > <mailto:23srishtigoel@gmail.com> > <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com>> > > <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com> > <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com>>> > > >>>> <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com> > <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com>> > > <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com> > <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com>>>>> wrote: > > >>>> > > >>>>> Hi Bruce, > > >>>>> > > >>>>> Thanks so much for pointing that > out, I > totally > > missed > > >>>>> that part. > > >>>>> > > >>>>> Also, the registration definitely > isn't > appropriate. > > >>>>> Could someone please guide me how to > correct this > > >>>>> problem. I have attached a > screenshot of > how it > > looks > > >>>>> like currently. > > >>>>> > > >>>>> > > >>>>> <Screen Shot 2018-04-08 at 2.53.33 > PM.png> > > >>>>> > > >>>>> Best, > > >>>>> Srishti > > >>>>> Social/Clinical Research Specialist > > >>>>> Child Imaging Research and Life > Experiences Lab > > >>>>> University of North Carolina at > Chapel Hill > > >>>>> email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>> > > >>>>> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>>> > > > >>>>> skype: srishti.goel12 > > >>>>> > > >>>>> > > >>>>> On Sun, Apr 8, 2018 at 11:00 AM, > Bruce Fischl > > >>>>> <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> > > >>>>> <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>>> wrote: > > >>>>> > > >>>>> Hi Srishti > > >>>>> > > >>>>> the directory you are in doesn't > matter. YOu > > >>>>> either need to set SUBJECTS_DIR in the > > >>>>> environment, or use --sd <SUBJECTS_DIR> to > > specify the > > >>>>> directory that contains your subjects. I > > think you > > >>>>> can also give it the full path > to a target > > volume > > >>>>> if you want, but maybe Doug can > comment as he > > >>>>> knows this stuff better than I do > > >>>>> > > >>>>> cheers > > >>>>> Bruce > > >>>>> > > >>>>> > > >>>>> > > >>>>> On Sun, 8 Apr 2018, srishti > goel wrote: > > >>>>> > > >>>>> When I type this > command:tkregisterfv --mov > > >>>>> negative_allsocial_proportion.nii --regheader --s > > >>>>> mni152_subject --surfs --reg > > reg.deleteme.dat > > >>>>> > > >>>>> It gives me the error: cannot find > > mni152_subject. > > >>>>> Although I clearly checked that the > > directory > > >>>>> from which I am submitting this > command > > has the > > >>>>> mni152_subject directory within which there > > >>>>> are all the other required > directories such > > >>>>> as: mri, > > >>>>> stats, surf, scripts, etc. > > >>>>> > > >>>>> I am unsure what is happening here. > > >>>>> > > >>>>> > > >>>>> Best, > > >>>>> Srishti > > >>>>> Social/Clinical Research Specialist > > >>>>> Child Imaging Research and Life > > Experiences Lab > > >>>>> University of North Carolina at Chapel Hill > > >>>>> email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>> > > >>>>> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>>> > > >>>>> skype: srishti.goel12 > > >>>>> > > >>>>> > > >>>>> On Thu, Apr 5, 2018 at > 12:49 PM, > Douglas N. > > >>>>> Greve <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>> > > >>>>> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>>> wrote: > > >>>>> Those commands look ok. My suspicion > > >>>>> goes to the use of --regheader. See > > >>>>> whether the registration is ok with > > >>>>> > > >>>>> tkregisterfv --mov > > >>>>> negative_allsocial_proportion.nii --regheader --s > > >>>>> mni152_subject --surfs --reg > > reg.deleteme.dat > > >>>>> > > >>>>> > > >>>>> On 04/05/2018 08:34 AM, srishti > > goel wrote: > > >>>>> > Hi, > > >>>>> > > > >>>>> > I am trying to compare my volume > > maps > > >>>>> > > > (negative_allsocial_proportion.nii) to > > >>>>> someone else's > > >>>>> > (SN_like_cortical_lh.nii.gz) who > > have > > >>>>> it on a surface > > >>>>> > (mni152_subject). So I used the > > steps > > >>>>> for mri_vol2surf command as > > >>>>> > follows: > > >>>>> > > > >>>>> > Commands: > > >>>>> > mri_vol2surf --src > > >>>>> negative_allsocial_proportion.nii --regheader > > >>>>> > mni152_subject --hemi lh --o > > >>>>> ./neg_allsocial_lh.nii --projfrac 0.5 > > >>>>> > Then to view it: > > >>>>> > tksurfer mni152_subject lh inflated > > >>>>> -overlay ./neg_allsocial_lh.nii > > >>>>> > -overlay SN_like_cortical_lh.nii.gz > > >>>>> -fthresh 0.5 > > >>>>> > > > >>>>> > Everything ran fine and we > > didn't get > > >>>>> any error but then while viewing > > >>>>> > the files we could not see our map > > >>>>> (neg_allsocail_lh.nii) on the > > >>>>> > surface. This file seemed to > > work fine > > >>>>> as it is not an empty file when > > >>>>> > I checked the file size. > > However, when > > >>>>> we view it using tksurfer it > > >>>>> > does not show up as a highlighted > > >>>>> portion on the surface. The > > >>>>> > SN_like_cortical_lh.nii.gz file > > shows > > >>>>> up just fine. > > >>>>> > > > >>>>> > Could someone please help me figure > > >>>>> out what might have gone wrong here. > > >>>>> > > > >>>>> > Thanks so much! > > >>>>> > > > >>>>> > > > >>>>> > > > >>>>> > > > _______________________________________________ > > >>>>> > Freesurfer mailing list > > >>>>> > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>>>> > > > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >>>>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > >>>>> > > >>>>> _______________________________________________ > > >>>>> Freesurfer mailing list > > >>>>> Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >>>>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>>> > > >>>>> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <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(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >>>>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>>> > > >>>>> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <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(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >>>>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > >>>> > > >>>> > > >>>> _______________________________________________ > > >>>> Freesurfer mailing list > > >>>> Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >>>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > >>> > > >>> > > >>> _______________________________________________ > > >>> Freesurfer mailing list > > >>> Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>>> > > >>> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <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(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > >> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>>> > > >> <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <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(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > ... > > [Message clipped] > >

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