Hi Zeke, That resolved the issue. Thank you very much.
Warmest Regards, Anderson Napolitano ________________________________________ From: [email protected] <[email protected]> on behalf of [email protected] <[email protected]> Sent: Wednesday, January 18, 2017 10:00 AM To: [email protected] Subject: Freesurfer Digest, Vol 155, Issue 27 Send Freesurfer mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. installation fail :( (Shapiro, Allison L) 2. Re: TRACULA in FreeSurfer 6.0 trac-paths error (Derek A Pisner) 3. PETSURFER Tutorial Problems <Repost> (Anderson Napolitano) 4. question about cortical volume group analyses (Ritobrato Datta) 5. Re: V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream (Antonin Skoch) 6. FS Anatomic ROIs Atlas (Da, Xiao) 7. Anatomical ROI parcellation (Aya Kabbara) 8. Re: Anatomical ROI parcellation (Anthony Dick) 9. Re: FS Anatomic ROIs Atlas (Douglas N Greve) 10. Re: V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream (Antonin Skoch) 11. WM lobes and Corpus Callosum (Bharadwaj, Pradyumna - (prad)) 12. Re: WM lobes and Corpus Callosum (Yendiki, Anastasia) 13. Re: mri_vol2surf (Zhivago) 14. 'nuisance factors adjusted' values ([email protected]) 15. recon-all error (Freesurfer) ( Gwang-Won Kim ) 16. Question (N Saf) 17. Re: mri_vol2surf (Bruce Fischl) 18. Neuroimaging postdoctoral position (Tiril Pedersen Gurholt) 19. Re: Question (Bruce Fischl) 20. mris_make_surfaces error with bbr-init-header (Sneha Pandya) 21. Re: mris_make_surfaces error with bbr-init-header (Bruce Fischl) 22. Re: Fwd: QDEC versus Terminal annotation (Douglas N Greve) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Jan 2017 16:50:29 +0000 From: "Shapiro, Allison L" <[email protected]> Subject: [Freesurfer] installation fail :( To: "[email protected]" <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" Dear FreeSurfer support, I am a new user of the Freesurfer program and attempted to install everything this morning on my Mac OSx 10.11.6 (El Capitan). To preface everything, I updated my XQuartz program before installing, and I do not have Matlab on this computer and understand that I can?t use the fMRI functionality without this, but this is not my goal. The installation appeared to go as planned, but when I went to test the installation with the commands: $> <source_freesurfer> $> freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red I received the following error: -bash: $: command not found I was not able to decipher this error with The Google, so I am hoping that you can help. Thank you so much for your time! Best Wishes, Allie Allison L B Shapiro, MPH, PhD Postdoctoral Research Fellow LEAD Center | Colorado School of Public Health Office 303.724.7708 ?Those who dare to fail miserably can achieve greatly? - JFK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170117/b75299a3/attachment-0001.html ------------------------------ Message: 2 Date: Tue, 17 Jan 2017 11:20:53 -0600 From: Derek A Pisner <[email protected]> Subject: Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error To: Freesurfer support list <[email protected]> Message-ID: <cagvsa9scxzfasfdb5x+2oanc5ag6_vgohewvpvwzu2kvbe8...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Thanks Anastasia! You seemed to have caught the issue. the dtifit files were mistakenly generated from the anisotropic preprocessed image. I will ensure the same voxel dimensions among all inputs and re-run. Will let you know if that doesn't fix it! All the best, Derek On Tue, Jan 17, 2017 at 10:31 AM, Yendiki, Anastasia < [email protected]> wrote: > Hi Derek - There's an inconsistency among the output volumes that are > supposed to be in diffusion space; some have 2mm iso resolution and some > have .9x.9x3mm. From the logs it looks like you reran some of the > pre-processing steps separately. If you ran some before resampling and some > after, this may be causing the mix-up. I would just start from scratch in a > new subject directory and see if that fixes it. > > Best, > a.y > > ------------------------------ > *From:* [email protected] [ > [email protected]] on behalf of Derek A Pisner [ > [email protected]] > *Sent:* Sunday, January 15, 2017 3:01 PM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error > > Uploaded: > > https://gate.nmr.mgh.harvard.edu/filedrop2/index.php?p=6cwuw1zwaag > > Also, I've included a dwi_TRfixed.nii.gz file with the TR in the header > fixed. Curious to see if that one works! > > mri_convert --in_type nii --out_type nii --out_orientation RAS dwi.nii.gz > -tr 1000 dwi_TRfixed.nii.gz > > On Sun, Jan 15, 2017 at 1:44 PM, Yendiki, Anastasia < > [email protected]> wrote: > >> Hi Derek - It looks like it fails, but I suspect that it may be something >> unrelated to the warning. Can you please upload a zip file with this >> subject's TRACULA directories (dmri, dmri.bedpostX, dlabel, dpath, scripts) >> for me here: >> >> https://gate.nmr.mgh.harvard.edu/filedrop2/ >> >> Thanks! >> >> a.y >> >> ------------------------------ >> *From:* [email protected] [ >> [email protected]] on behalf of Derek A Pisner [ >> [email protected]] >> *Sent:* Sunday, January 15, 2017 2:36 PM >> *To:* Freesurfer support list >> >> *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error >> >> Hi Anastasia, >> >> >> >> See attached log. Hard to tell, but it does seem that trac-all fails >> after this warning. >> >> >> >> Thanks for taking a look! >> >> >> >> Derek Pisner >> >> Doctoral Student >> >> CLA 4.600 >> >> Mood Disorders Laboratory (MDL) >> >> Department of Psychology | The University of Texas at Austin >> >> >> >> On Sun, Jan 15, 2017 at 1:27 PM, Yendiki, Anastasia < >> [email protected]> wrote: >> >>> Hi Derek - It sounds like the programs that you used to convert from >>> dicom to nifti and to resample from anisotropic nifti to isotropic nifti >>> don't copy the TE and TR info in the header correctly. This information is >>> not needed to run -paths, however. Does trac-all stop running after this >>> warning, or does it keep going? Can you attach your entire trac-all.log >>> file? Thanks! >>> >>> a.y >>> >>> ------------------------------ >>> *From:* [email protected] [ >>> [email protected]] on behalf of Derek A Pisner [ >>> [email protected]] >>> *Sent:* Sunday, January 15, 2017 11:47 AM >>> *To:* [email protected] >>> *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error >>> >>> Hi Anastasia, >>> >>> Thanks for the quick response! >>> >>> The TE and the TR are both listed as 0.00 with mri_info. Of note, these >>> dwi images have been resampled from anisotropic to isotropic voxels using >>> an in-house python script. I noticed that this error comes up only for the >>> resampled, but not the original image. I am guessing this is the underlying >>> source of the problem and has less to do with trac-all. What does trac-all >>> need from the header to successfully run -paths? How can the header be >>> corrected in freesurfer so that it will run successfully? Strangely, the TE >>> also comes up as being equal to 0 in the original, anisotropic, image... >>> The TR is what appears to be different and perhaps that is the source of >>> the niiRead() warning? See below. >>> >>> Many Thanks, >>> >>> Derek >>> >>> *vlogin03.ls5(69)$ *mri_info dwi.nii.gz >>> >>> niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm >>> >>> WARNING: niiRead(): unknown time units 0 in >>> /work/04171/dpisner/data/ABM/TRACULA/tractography_output/s00 >>> 2/dmri/dwi.nii.gz >>> >>> Volume information for dwi.nii.gz >>> >>> type: nii >>> >>> dimensions: 115 x 115 x 56 x 55 >>> >>> voxel sizes: 2.000000, 2.000000, 2.000000 >>> >>> type: FLOAT (3) >>> >>> fov: 230.000 >>> >>> dof: 0 >>> >>> xstart: -115.0, xend: 115.0 >>> >>> ystart: -115.0, yend: 115.0 >>> >>> zstart: -56.0, zend: 56.0 >>> >>> * TR: 0.00 msec, TE: 0.00 msec,* TI: 0.00 msec, flip angle: >>> 0.00 degrees >>> >>> nframes: 55 >>> >>> PhEncDir: UNKNOWN >>> >>> FieldStrength: 0.000000 >>> >>> ras xform present >>> >>> xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = >>> -0.4490 >>> >>> : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = >>> 40.5440 >>> >>> : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = >>> 55.0398 >>> >>> Orientation : LAS >>> >>> Primary Slice Direction: axial >>> >>> >>> voxel to ras transform: >>> >>> -2.0000 0.0000 0.0000 114.5510 >>> >>> 0.0000 2.0000 0.0000 -74.4560 >>> >>> 0.0000 0.0000 2.0000 -0.9602 >>> >>> 0.0000 0.0000 0.0000 1.0000 >>> >>> >>> voxel-to-ras determinant -8 >>> >>> >>> ras to voxel transform: >>> >>> -0.5000 -0.0000 -0.0000 57.2755 >>> >>> -0.0000 0.5000 -0.0000 37.2280 >>> >>> -0.0000 -0.0000 0.5000 0.4801 >>> >>> -0.0000 -0.0000 -0.0000 1.0000 >>> >>> >>> *vlogin03.ls5(84)$ *mri_info aniso_eddy_corrected_data_denoised.nii.gz >>> >>> Volume information for eddy_corrected_data_denoised.nii.gz >>> >>> type: nii >>> >>> dimensions: 256 x 256 x 37 x 55 >>> >>> voxel sizes: 0.898400, 0.898400, 3.000002 >>> >>> type: FLOAT (3) >>> >>> fov: 229.990 >>> >>> dof: 0 >>> >>> xstart: -115.0, xend: 115.0 >>> >>> ystart: -115.0, yend: 115.0 >>> >>> zstart: -55.5, zend: 55.5 >>> >>> * TR: 1000.00 msec, TE: 0.00 msec,* TI: 0.00 msec, flip >>> angle: 0.00 degrees >>> >>> Yendiki, Anastasia >>> <https://www.mail-archive.com/[email protected]&q=from:%22Yendiki%2C+Anastasia%22> >>> Fri, 13 Jan 2017 07:12:39 -0800 >>> <https://www.mail-archive.com/[email protected]&q=date:20170113> >>> >>> Hi Derek - Thanks for testing the 6.0 release candidate. Does it keep >>> running >>> after this message? Since this is a warning and not an error, it may not be >>> critical. If you run mri_info on your dwi.nii.gz, does the TE show up as >>> zero? >>> >>> Best, >>> a.y >>> >>> >>> >>> On Thu, Jan 12, 2017 at 9:06 PM, Derek A Pisner <[email protected]> >>> wrote: >>> >>>> Hi Anastasia, >>>> >>>> I am getting the following error when running trac-all ?paths on all of >>>> my diffusion images using the newly updated TRACULA: >>>> >>>> *vlogin03.ls5(97)$* /work/04171/dpisner/stampede/A >>>> pplications/freesurfer/bin/trac-all -no-isrunning -path -c >>>> /work/04171/dpisner/data/ABM/TRACULA/tractography_output/s00 >>>> 2/trac_config.txt >>>> >>>> niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm >>>> >>>> WARNING: niiRead(): unknown time units 0 in >>>> /work/04171/dpisner/data/ABM/TRACULA/tractography_output/s00 >>>> 2/dmri/dwi.nii.gz >>>> >>>> >>>> >>>> Any idea what?s going on here? >>>> >>>> >>>> >>>> Thanks as always, >>>> >>>> >>>> >>>> Derek Pisner >>>> >>>> Doctoral Student >>>> >>>> CLA 4.600 >>>> >>>> Mood Disorders Laboratory (MDL) >>>> >>>> Department of Psychology | The University of Texas at Austin >>>> >>>> >>>> >>>> P.S. Here is the header information on my dwi.nii.gz file: >>>> >>>> *vlogin03.ls5(105)$* fslhd dwi.nii.gz >>>> >>>> filename dwi.nii.gz >>>> >>>> sizeof_hdr 348 >>>> >>>> data_type FLOAT32 >>>> >>>> dim0 4 >>>> >>>> dim1 115 >>>> >>>> dim2 115 >>>> >>>> dim3 56 >>>> >>>> dim4 55 >>>> >>>> dim5 1 >>>> >>>> dim6 1 >>>> >>>> dim7 1 >>>> >>>> vox_units Unknown >>>> >>>> time_units Unknown >>>> >>>> datatype 16 >>>> >>>> nbyper 4 >>>> >>>> bitpix 32 >>>> >>>> pixdim0 0.000000 >>>> >>>> pixdim1 2.000000 >>>> >>>> pixdim2 2.000000 >>>> >>>> pixdim3 2.000000 >>>> >>>> pixdim4 1.000000 >>>> >>>> pixdim5 1.000000 >>>> >>>> pixdim6 1.000000 >>>> >>>> pixdim7 1.000000 >>>> >>>> vox_offset 352 >>>> >>>> cal_max 0.0000 >>>> >>>> cal_min 0.0000 >>>> >>>> scl_slope 1.000000 >>>> >>>> scl_inter 0.000000 >>>> >>>> phase_dim 0 >>>> >>>> freq_dim 0 >>>> >>>> slice_dim 0 >>>> >>>> slice_name Unknown >>>> >>>> slice_code 0 >>>> >>>> slice_start 0 >>>> >>>> slice_end 0 >>>> >>>> slice_duration 0.000000 >>>> >>>> time_offset 0.000000 >>>> >>>> intent Unknown >>>> >>>> intent_code 0 >>>> >>>> intent_name >>>> >>>> intent_p1 0.000000 >>>> >>>> intent_p2 0.000000 >>>> >>>> intent_p3 0.000000 >>>> >>>> qform_name Unknown >>>> >>>> qform_code 0 >>>> >>>> qto_xyz:1 2.000000 0.000000 0.000000 0.000000 >>>> >>>> qto_xyz:2 0.000000 2.000000 0.000000 0.000000 >>>> >>>> qto_xyz:3 0.000000 0.000000 2.000000 0.000000 >>>> >>>> qto_xyz:4 0.000000 0.000000 0.000000 1.000000 >>>> >>>> qform_xorient Left-to-Right >>>> >>>> qform_yorient Posterior-to-Anterior >>>> >>>> qform_zorient Inferior-to-Superior >>>> >>>> sform_name Aligned Anat >>>> >>>> sform_code 2 >>>> >>>> sto_xyz:1 -2.000000 0.000000 0.000000 114.551003 >>>> >>>> sto_xyz:2 0.000000 2.000000 0.000000 -74.456001 >>>> >>>> sto_xyz:3 0.000000 0.000000 2.000000 -0.960182 >>>> >>>> sto_xyz:4 0.000000 0.000000 0.000000 1.000000 >>>> >>>> sform_xorient Right-to-Left >>>> >>>> sform_yorient Posterior-to-Anterior >>>> >>>> sform_zorient Inferior-to-Superior >>>> >>>> file_type NIFTI-1+ >>>> >>>> file_code 1 >>>> >>>> descrip >>>> >>>> aux_file >>>> >>>> -- >>>> Derek Pisner >>>> >>> >>> >>> >>> -- >>> Derek Pisner >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> 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. >>> >>> >> >> >> -- >> Derek Pisner >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> 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. >> >> > > > -- > Derek Pisner > > _______________________________________________ > Freesurfer mailing list > [email protected] > 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. > > -- Derek Pisner -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170117/d912cb6d/attachment-0001.html ------------------------------ Message: 3 Date: Tue, 17 Jan 2017 19:04:53 +0000 From: Anderson Napolitano <[email protected]> Subject: [Freesurfer] PETSURFER Tutorial Problems <Repost> To: "[email protected]" <[email protected]> Cc: Colin Wilson <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" Good Afternoon Support Team, Per step one of your PETSURFER tutorial, the command: gtmseg --s <subject>?, where the <subject> is the name of the subject that we had ran recon-all, outputs the error as described in out.txt attached in this email. If you have the time, it would be much appreciated if you can help us resolve this issue. Thank you for your time. Warmest Regards, Anderson Napolitano? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170117/586cf85e/attachment-0001.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: out.txt Url: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170117/586cf85e/attachment-0001.txt ------------------------------ Message: 4 Date: Tue, 17 Jan 2017 14:05:10 -0500 (EST) From: Ritobrato Datta <[email protected]> Subject: [Freesurfer] question about cortical volume group analyses To: Freesurfer support list <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset=utf-8 Hi All, I have a analysed data from AD patients and healthy controls and want to do a group analyses of cortical volume. I have run qcache on each subject. In the lh.volume.fsaverage.mris_preproc.log file, mri_surf2surf --srcsubject AD1 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.76769/AD1.1.mgh --sval /Applications/freesurfer5.1/subjects/AD1/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex what does -jac jacobian correction mean ? Is it accounting/correcting for differences in hemispheric volume ? I want to do a group analyses between AD and controls for cortical volume, can I just use the lh.volume.fwhm??.fsaverage.mgh at different smoothing kernels ? Do I need to correct for whole brain volume or some scaling or is it already taken care of ? Are there references that have used free surfer to report group analyses for cortical volume ? Can someone point to a few ? Thanks Ri ------------------------------ Message: 5 Date: Tue, 17 Jan 2017 21:37:49 +0100 From: Antonin Skoch <[email protected]> Subject: Re: [Freesurfer] V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" Dear Martin, thank you for the feedback. I read the wiki but the instructions concerning aseg edits were not much clear for me. And, I was misinformed by -noasegfusion option. The pity with aseg errors is that with the current design and when the error is large to affect surfaces in base, it is necessary to edit the same error twice. Since the aseg of base is not initialized from cross, and long is not initialized from base, then one has to edit the same error both in base and in long (or cross). If there is a systematic error which affects all timepoints (as it is in my case - I have 2 points), I effectively have to edit the same error 3 times. It is quite large error affecting whole posterior part of lateral ventricle (see screenshot). Therefore, I thought that best option would be to edit the base and initialize long from base using -noasegfusion. I tried to do that by manually copying aseg from base and manually running mri_ca_label with -r and -ri option (and and the error is (almost) cleaned in long. Why do you think that the initialization from base is worse/undesirable than initialization from fused aseg from cross? It seems to me that to initialize from fused (averaged) asegs of cross or initialize from aseg of base (which is averaged template of cross) is methodologically quite similar, should produce similar results and in terms of edits it is much more convenient way. Regards, Antonin Hi Antonin, the -noasegfusion is not really supported and a left over from initial testing when we first developed the stream. I will take a look at it and probably remove the flag (or implement it in a way that it really initializes with the aseg from the base, although I think this is not desirable, unless one really assumes there is no/ or very little change between time points. About aseg edits in longitudinal processing, please look at our edit wiki page: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#aseg.mgz <https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#aseg.mgz> ? ASEG edits can be done in cross, base and long. Recommendation: Edit in long only if you want to correct the volume of important structures. Edit in base if surfaces need to be changed due to incorrect labeling of aseg. Not necessary to edit in cross. The segmentation in the long runs is initialized with a fused aseg (a weighted average of the cross sectional asegs). Thus any edits done to the cross sectionals are incorporated indirectly into the long stream. But since the fused aseg is used only for the initialization, it can happen that manual edits from the cross get removed again. Therefore, to correct the volume, just edit the long." So for your ventricle correction, you could either clean up the cross data and hope it caries over to the long (it should), or directly edit the long aseg. Best, Martin > On 16 Jan 2017, at 23:23, Antonin Skoch <[email protected]> wrote: > > Dear experts, > > I am testing the longitudinal stream with V6beta version. > > The recon-all -help says for -noasegfusion: > > Do not create 'fused' aseg from the longbase timepoints, which would normally > be used to initialize the ca_labeling. Instead, initialize using the longbase > aseg.mgz. > > As I looked to recon-all code it seems that in case of -noasegfusion there is > no use of -r and -ri parameters and therefore no "initialization". Could you > please comment on? > > My second query is regarding manual edits: > > In one subject the manual editing of aseg was necessary due to ventricle > mislabeling. I edited the aseg.presurf in base template and subsequently run > longitudinal stream via > > recon-all -long tpID templateID -noasegfusion -all > > From the last sentence of -noasegfusion help I (wrongly) expected that my > aseg.presurf edits in base template would be incorporated for -long recon. > However, this was not the case, the edits have not been incorporated at all. > Looking at the recon-all code the aseg.presurf from base is never used for > -long. > > I thought that I could incorporate manual edits from base by manual copying > of aseg.presurf from base to long directory. As I looked for the way how the > manual aseg edits are handled in recon-all, they are identified by using the > difference between the files aseg.auto and aseg.manedit which contains manual > edits. Therefore I think that the copying from base is not an option, I > expect that this would replace segmentations not only in manual edit regions, > but in all regions where the aseg.auto of base and aseg.auto of -long differs > (they do not have the same input) which is undesirable. So I think I do not > have any other option than to edit aseg.presurf in -long again. > > Could you please comment on how to optimally handle such situations? > > Regards, > > Antonin Skoch > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170117/a8d9580c/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: aseg_error.png Type: image/png Size: 25533 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170117/a8d9580c/attachment-0001.png ------------------------------ Message: 6 Date: Tue, 17 Jan 2017 21:35:09 +0000 From: "Da, Xiao" <[email protected]> Subject: [Freesurfer] FS Anatomic ROIs Atlas To: "'[email protected]'" <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii" Dear Freesurfer Community, I am wondering if you have these anatomic ROIs (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation) already done for the 3D volumetric standard MNI brain (either ch2 single subject brain(preferred) or 152 average brain) Greatly appreciated it. Thanks and best regards, Xiao Da Biomedical Engineer - Programmer Analyst II Functional Neuroimaging Laboratory Brigham and Women's Hospital 221 Longwood Avenue, Braunwald Building, Room LM116 Boston, MA 02115 [email protected]<mailto:[email protected]> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170117/fcf3460e/attachment-0001.html ------------------------------ Message: 7 Date: Tue, 17 Jan 2017 21:47:47 +0000 From: Aya Kabbara <[email protected]> Subject: [Freesurfer] Anatomical ROI parcellation To: "[email protected]" <[email protected]> Message-ID: <db5pr04mb16853c4ea510193cde7155c59a...@db5pr04mb1685.eurprd04.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Dear Freesurfer team, I am wondering is there a way using tksurfer to edit a given atlas (for example: destrieux atlas). I would like to parcellate the superior temporal region into three regions . Is there a way to do that? Thank you Aya -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170117/da400483/attachment-0001.html ------------------------------ Message: 8 Date: Tue, 17 Jan 2017 16:56:18 -0500 From: Anthony Dick <[email protected]> Subject: Re: [Freesurfer] Anatomical ROI parcellation To: <[email protected]>, <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="windows-1252" https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit On 1/17/17 4:47 PM, Aya Kabbara wrote: > > Dear Freesurfer team, > > > I am wondering is there a way using tksurfer to edit a given atlas > (for example: destrieux atlas). > > I would like to parcellate the superior temporal region into three > regions . > > > Is there a way to do that? > > > Thank you > > Aya > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > 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. -- Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: [email protected] Webpage: http://myweb.fiu.edu/adick Join the Society for the Study of Human Development: http://www.sshdonline.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170117/a5f1435f/attachment-0001.html ------------------------------ Message: 9 Date: Tue, 17 Jan 2017 17:04:21 -0500 From: Douglas N Greve <[email protected]> Subject: Re: [Freesurfer] FS Anatomic ROIs Atlas To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=windows-1252; format=flowed Try running recon-all on the mni152 brain On 01/17/2017 04:35 PM, Da, Xiao wrote: > > Dear Freesurfer Community, > > I am wondering if you have these anatomic ROIs > (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation) > already done for the 3D volumetric standard MNI brain (either ch2 > single subject brain(preferred) or 152 average brain) > > Greatly appreciated it. > > Thanks and best regards, > > *Xiao Da* > > Biomedical Engineer - Programmer Analyst II > > Functional Neuroimaging Laboratory > > Brigham and Women?s Hospital > > 221 Longwood Avenue, Braunwald Building, Room LM116 > > Boston, MA 02115 > > /[email protected] <mailto:[email protected]>/ > > // > > // > > // > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ Message: 10 Date: Tue, 17 Jan 2017 23:14:53 +0100 From: Antonin Skoch <[email protected]> Subject: Re: [Freesurfer] V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" Dear Martin, one more thing: When the error is large and present in both timepoints (as is my case), I think that necessity of editing the same error in both timepoints can easily lead to error (maybe even demonstrated as false positive effect) caused by non-systematic editing. When editing comprises many voxels one cannot realistically assure the perfect consistence in editing. Editing only once (in base) and initialize mri_ca_label in long from base can avoid this problem. So I think the initialization of mri_ca_label from base is not a bad option for such cases. What do you think? Antonin Hi Antonin, the -noasegfusion is not really supported and a left over from initial testing when we first developed the stream. I will take a look at it and probably remove the flag (or implement it in a way that it really initializes with the aseg from the base, although I think this is not desirable, unless one really assumes there is no/ or very little change between time points. About aseg edits in longitudinal processing, please look at our edit wiki page: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#aseg.mgz <https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#aseg.mgz> ? ASEG edits can be done in cross, base and long. Recommendation: Edit in long only if you want to correct the volume of important structures. Edit in base if surfaces need to be changed due to incorrect labeling of aseg. Not necessary to edit in cross. The segmentation in the long runs is initialized with a fused aseg (a weighted average of the cross sectional asegs). Thus any edits done to the cross sectionals are incorporated indirectly into the long stream. But since the fused aseg is used only for the initialization, it can happen that manual edits from the cross get removed again. Therefore, to correct the volume, just edit the long." So for your ventricle correction, you could either clean up the cross data and hope it caries over to the long (it should), or directly edit the long aseg. Best, Martin > On 16 Jan 2017, at 23:23, Antonin Skoch <[email protected]> wrote: > > Dear experts, > > I am testing the longitudinal stream with V6beta version. > > The recon-all -help says for -noasegfusion: > > Do not create 'fused' aseg from the longbase timepoints, which would normally > be used to initialize the ca_labeling. Instead, initialize using the longbase > aseg.mgz. > > As I looked to recon-all code it seems that in case of -noasegfusion there is > no use of -r and -ri parameters and therefore no "initialization". Could you > please comment on? > > My second query is regarding manual edits: > > In one subject the manual editing of aseg was necessary due to ventricle > mislabeling. I edited the aseg.presurf in base template and subsequently run > longitudinal stream via > > recon-all -long tpID templateID -noasegfusion -all > > From the last sentence of -noasegfusion help I (wrongly) expected that my > aseg.presurf edits in base template would be incorporated for -long recon. > However, this was not the case, the edits have not been incorporated at all. > Looking at the recon-all code the aseg.presurf from base is never used for > -long. > > I thought that I could incorporate manual edits from base by manual copying > of aseg.presurf from base to long directory. As I looked for the way how the > manual aseg edits are handled in recon-all, they are identified by using the > difference between the files aseg.auto and aseg.manedit which contains manual > edits. Therefore I think that the copying from base is not an option, I > expect that this would replace segmentations not only in manual edit regions, > but in all regions where the aseg.auto of base and aseg.auto of -long differs > (they do not have the same input) which is undesirable. So I think I do not > have any other option than to edit aseg.presurf in -long again. > > Could you please comment on how to optimally handle such situations? > > Regards, > > Antonin Skoch > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170117/2dc058e5/attachment-0001.html ------------------------------ Message: 11 Date: Tue, 17 Jan 2017 22:37:25 +0000 From: "Bharadwaj, Pradyumna - (prad)" <[email protected]> Subject: [Freesurfer] WM lobes and Corpus Callosum To: "[email protected]" <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" Hi, I've been trying to create WM lobes using the following steps: 1) mri_annotation2label --lobesStrict 2) Outputting the labels from step 1, & creating a simpler annotation without limbic and insular lobes 3) Labeling the WM using mri_aparc2aseg (mri_aparc2aseg --s MySub --annot Step2AnnotationFile --labelwm --hypo-as-wm --wmpar-dmax 20 --rip-unknown However, as the corpus callosum is not labelled as wm, it is not included in any WM lobe. Is there any workaround to assigning the corpus callosum to the different WM lobes or do I have to manually edit aseg.mgz to change the corpus callosum's value to match that of WM ? Thanks, -Prad -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170117/ac773d04/attachment-0001.html ------------------------------ Message: 12 Date: Wed, 18 Jan 2017 00:05:52 +0000 From: "Yendiki, Anastasia" <[email protected]> Subject: Re: [Freesurfer] WM lobes and Corpus Callosum To: Freesurfer support list <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" Hi Prad - mri_aparc2aseg assigns WM voxels to the nearest cortical region from the cortical parcellation. Which cortical region would you want to assign the corpus callosum to? What's labeled as corpus callosum in the aseg is the part of the corpus callosum between the 2 hemis. Best, a.y ________________________________ From: [email protected] [[email protected]] on behalf of Bharadwaj, Pradyumna - (prad) [[email protected]] Sent: Tuesday, January 17, 2017 5:37 PM To: [email protected] Subject: [Freesurfer] WM lobes and Corpus Callosum Hi, I've been trying to create WM lobes using the following steps: 1) mri_annotation2label --lobesStrict 2) Outputting the labels from step 1, & creating a simpler annotation without limbic and insular lobes 3) Labeling the WM using mri_aparc2aseg (mri_aparc2aseg --s MySub --annot Step2AnnotationFile --labelwm --hypo-as-wm --wmpar-dmax 20 --rip-unknown However, as the corpus callosum is not labelled as wm, it is not included in any WM lobe. Is there any workaround to assigning the corpus callosum to the different WM lobes or do I have to manually edit aseg.mgz to change the corpus callosum's value to match that of WM ? Thanks, -Prad -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170118/3414f4a7/attachment-0001.html ------------------------------ Message: 13 Date: Wed, 18 Jan 2017 11:56:40 +0530 From: Zhivago <[email protected]> Subject: Re: [Freesurfer] mri_vol2surf To: Freesurfer support list <[email protected]> Message-ID: <CAG0zojmbdJSAHjLJngi50emXfTURukQN9AkEvGFsNhhmiYKc=a...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi, >From whatever I read, there seem to be 2 ways for overlaying activation maps on surfaces. 1) automatic/manual registration of activation volume to orig.mgz and usage of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be overlaid on an inflated surface in freeview or tksurfer using the register.dat. 2) automatic/manual registration of activation volume to orig.mgz and overlay the activation volume on the inflated surface in tksurfer using the register.dat I want to know if both these are valid methods and if so, what are the pros and cons of each. Seems like mri_vol2surf lets us decide what part of the volume should be projected on the surface using the projfac arguments. But the direct volume overlay in tksurfer doesn't provide that option. In that case what part of the volume is projected on to the surface? Thanks, Zhivago... On Sun, Jan 15, 2017 at 10:12 PM, Zhivago <[email protected]> wrote: > Thanks Bruce! Appreciate all the help, > > On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl <[email protected] > > wrote: > >> 1) This is up to you. Jon Polimeni had a nice paper describing the >> trade-off between accurately representing the local neural response (which >> is best at the white border) and statistical power (which is best nearer >> the pial surface). >> >> 2) This is also up to you.Read the help in mri_vol2surf. e.g.: >> >> mri_vol2surf --help >> . >> . >> . >> --projfrac-avg min max del : average along normal >> >> 3) it is the way that we support. >> >> >> cheers >> Bruce >> >> >> On Sun, 15 Jan 2017, Zhivago wrote: >> >> Hey Bruce, >>> >>> Thank you very much for the responses! Had posted a couple of more >>> questions, but looks like it hasn't gone across. Will really appreciate >>> it >>> if you can provide some answers to these. >>> >>> 1) The mri_vol2surf is used to project the activations from the GM onto >>> an >>> inflated surface, which is usually the inflated smoothwm surface output >>> from >>> reconall. Will it be more accurate to use the inflated version of the >>> intermediate surface, like halfway between the white and pial matter? >>> Will >>> it make any kind of sense? >>> >>> 2) When mri_vol2surf projects a volume to a surface, does it average the >>> activation values of voxels along the cortical depth or sum it? What >>> really >>> happens beneath? Any amount of insight will be helpful. >>> >>> 3) Is mri_vol2surf the only way to view activation maps on inflated >>> surfaces >>> or any surface? >>> >>> Cheers, >>> Zhivago... >>> >>> On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl < >>> [email protected]> >>> wrote: >>> Hi Zhivago >>> >>> 1) You can project from inside the ?h.white surface if >>> projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't >>> make much sense though as it starts to get arbitrary. >>> >>> 2) The default projfrac, as documented in the -help response, is >>> 0. >>> >>> 3) Yes, 0-->white matter boundary. 1--> pial boundary. >>> >>> 4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1 >>> vector, which is a scalar field over the surface. >>> >>> cheers >>> Bruce >>> >>> >>> >>> On Sun, 15 Jan 2017, Zhivago wrote: >>> >>> Hi, >>> >>> >>> I do not have a good understanding of the >>> mri_vol2surf command. >>> >>> 1) Can this only project the part of the volume that >>> lies between the white >>> & pial matter? >>> 2) What is the default projection parameter that it >>> uses? >>> 3) Does projection always start from the white >>> matter, i.e. is 0 the white >>> matter surface? >>> 4) What is the nature of the mgh file that is >>> created by: >>> mri_vol2surf --src mri/spmT_0002.img --regheader >>> s04 --interp nearest >>> --hemi lh --o lh.sig.mgh >>> >>> Thanks, >>> Zhivago... >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> 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 >> [email protected] >> 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. >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170118/a951e48b/attachment-0001.html ------------------------------ Message: 14 Date: Wed, 18 Jan 2017 15:39:52 +0900 From: <[email protected]> Subject: [Freesurfer] 'nuisance factors adjusted' values To: Freesurfer support list <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-2022-JP Dear experts, I have some questions. I did Qdec group analysis with three nuisance factors. And one region remained after FDR correction. Then I did 'mri_surfcluster' specifying the FDR-determined voxel-wise threshold as the --thmin. After that I ran 'mri_segstats' and got the values. 1)Are these values 'nuisance factors adjusted' values? 2)If not, is there a way to get 'nuisance factors adjusted' values using FreeSurfer? Best Regards, Hiroki ------------------------------ Message: 15 Date: Wed, 18 Jan 2017 18:12:53 +0900 From: " Gwang-Won Kim " <[email protected]> Subject: [Freesurfer] recon-all error (Freesurfer) To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170118/654bf78f/attachment-0001.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: recon-all.log Url: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170118/654bf78f/attachment-0001.pl -------------- next part -------------- A non-text attachment was scrubbed... Name: freesurfer_error.docx Type: application/unknown Size: 17974 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170118/654bf78f/attachment-0001.bin ------------------------------ Message: 16 Date: Wed, 18 Jan 2017 15:51:39 +0330 From: N Saf <[email protected]> Subject: [Freesurfer] Question To: Freesurfer support list <[email protected]> Message-ID: <CAPmqMe+=h=cnu5vxgz5_qgoaovtb9iqktea1eolmvgy+wcf...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear FreeSurfers, I have a question about aseg file. I load the aseg file of bert subject in itk-snap and read the volume for 17 and 53 label but it is a bit larger of the volume in bert stats file. I do the same for some of my subjects too and I see the same result .I don't know why it is like that ?would you please clear the reason for me.because I need to compare the FreeSurfer result and I should use of aseg file labels but I'm afraid the comparison I'm doing is not valid. Sincerely yours, Nazanin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170118/5ae42ac0/attachment-0001.html ------------------------------ Message: 17 Date: Wed, 18 Jan 2017 08:31:19 -0500 (EST) From: Bruce Fischl <[email protected]> Subject: Re: [Freesurfer] mri_vol2surf To: Freesurfer support list <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" Hi Zhivago tksurfer is deprecated and uses one of the methods available in mri_vol2surf, so our advice would be to use vol2surf cheers Bruce On Wed, 18 Jan 2017, Zhivago wrote: > [cleardot.gif] > Hi, > > From whatever I read, there seem to be 2 ways for overlaying activation maps > on surfaces. > > 1) automatic/manual registration of activation volume to orig.mgz and usage > of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be > overlaid on an inflated surface in freeview or tksurfer using the > register.dat. > > 2) automatic/manual registration of activation volume to orig.mgz and > overlay the activation volume on the inflated surface in tksurfer using the > register.dat > > I want to know if both these are valid methods and if so, what are the pros > and cons of each.? Seems like mri_vol2surf lets us decide what part of the > volume should be projected on the surface using the projfac arguments.? But > the direct volume overlay in tksurfer doesn't provide that option.? In that > case what part of the volume is projected on to the surface? > > Thanks, > Zhivago... > > On Sun, Jan 15, 2017 at 10:12 PM, Zhivago <[email protected]> wrote: > Thanks Bruce!? Appreciate all the help, > > On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl > <[email protected]> wrote: > 1) This is up to you. Jon Polimeni had a nice paper > describing the trade-off between accurately representing > the local neural response (which is best at the white > border) and statistical power (which is best nearer the > pial surface). > > 2) This is also up to you.Read the help in mri_vol2surf. > e.g.: > > mri_vol2surf --help > . > . > . > ? ?--projfrac-avg min max del : average along normal > > 3) it is the way that we support. > > cheers > Bruce > > > On Sun, 15 Jan 2017, Zhivago wrote: > > Hey Bruce, > > Thank you very much for the responses!? Had > posted a couple of more > questions, but looks like it hasn't gone > across.? Will really appreciate it > if you can provide some answers to these. > > 1) The mri_vol2surf is used to project the > activations from the GM onto an > inflated surface, which is usually the > inflated smoothwm surface output from > reconall.? Will it be more accurate to use the > inflated version of the > intermediate surface, like halfway between the > white and pial matter?? Will > it make any kind of sense? > > 2) When mri_vol2surf projects a volume to a > surface, does it average the > activation values of voxels along the cortical > depth or sum it?? What really > happens beneath?? Any amount of insight will > be helpful. > > 3) Is mri_vol2surf the only way to view > activation maps on inflated surfaces > or any surface? > > Cheers, > Zhivago... > > On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl > <[email protected]> > wrote: > ? ? ? Hi Zhivago > > ? ? ? 1) You can project from inside the > ?h.white surface if > ? ? ? projfrac<0 and outside pial if > projfrac>1. <<0 and >>1 won't > ? ? ? make much sense though as it starts to > get arbitrary. > > ? ? ? 2) The default projfrac, as documented > in the -help response, is > ? ? ? 0. > > ? ? ? 3) Yes, 0-->white matter boundary. 1--> > pial boundary. > > ? ? ? 4) The .mgh/.mgz file create by vol2surf > is an nvertices x 1 x 1 > ? ? ? vector, which is a scalar field over the > surface. > > ? ? ? cheers > ? ? ? Bruce > > > > ? ? ? On Sun, 15 Jan 2017, Zhivago wrote: > > ? ? ? ? ? ? Hi, > > > ? ? ? ? ? ? I do not have a good understanding > of the > ? ? ? ? ? ? mri_vol2surf command. > > ? ? ? ? ? ? 1) Can this only project the part > of the volume that > ? ? ? ? ? ? lies between the white > ? ? ? ? ? ? & pial matter? > ? ? ? ? ? ? 2) What is the default projection > parameter that it > ? ? ? ? ? ? uses? > ? ? ? ? ? ? 3) Does projection always start > from the white > ? ? ? ? ? ? matter, i.e. is 0 the white > ? ? ? ? ? ? matter surface? > ? ? ? ? ? ? 4) What is the nature of the mgh > file that is > ? ? ? ? ? ? created by: > ? ? ? ? ? ? mri_vol2surf --src > mri/spmT_0002.img --regheader > ? ? ? ? ? ? s04? --interp nearest > ? ? ? ? ? ? --hemi lh --o lh.sig.mgh > > ? ? ? ? ? ? Thanks, > ? ? ? ? ? ? Zhivago... > > > _______________________________________________ > Freesurfer mailing list > [email protected] > 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 > [email protected] > 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. > > > > > ------------------------------ Message: 18 Date: Wed, 18 Jan 2017 13:34:21 +0000 From: Tiril Pedersen Gurholt <[email protected]> Subject: [Freesurfer] Neuroimaging postdoctoral position To: "[email protected]" <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" Dear All, At the NORMENT ? K.G. Jebsen Research Centre for Psychosis Research, a Centre of Excellence, Institute of Clinical Medicine, University of Oslo, there is a position available as a postdoctoral student funded by the Research Council of Norway. The research area is psychiatric neuroimaging with focus on analysis of structural and functional, DTI and ASL MR imaging datasets with regard to developmental trajectories and genetic, environmental and phenotypic variation. Applicants should have a doctoral degree (PhD) in neuroimaging, computer science, bioinformatics, psychiatry, psychology or equivalent. Applicants who have handed in their dissertation for evaluation are also encouraged to apply, caveat the dissertation is approved. The application deadline is January 25, 2017. For further information and to submit an application please also see http://uio.easycruit.com/vacancy/1719677/70331?iso=no . Best regards, Tiril Gurholt --- Tiril Gurholt Postdoctoral Fellow Psychosis Research Centre, NORMENT Institute of Clinical Medicine, University of Oslo, Norway http://www.med.uio.no/norment/ [cid:[email protected]] -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170118/4a315088/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 5853 bytes Desc: image001.png Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170118/4a315088/attachment-0001.png ------------------------------ Message: 19 Date: Wed, 18 Jan 2017 08:48:46 -0500 (EST) From: Bruce Fischl <[email protected]> Subject: Re: [Freesurfer] Question To: Freesurfer support list <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" Hi Nazanin the volumes reported in the aseg.stats file have been corrected for partial volume effects. cheers Bruce On Wed, 18 Jan 2017, N Saf wrote: > Dear FreeSurfers, > I have a question about aseg file. I load the aseg file of bert subject in > itk-snap and read the volume for 17 and 53 label but it is a bit larger of > the volume in bert stats file. I do the same for some of my subjects too and > I see the same result .I don't know why it is like that ?would you please > clear the reason for me.because I need to ?compare the FreeSurfer result and > I should use of aseg file labels but I'm afraid the comparison I'm doing is > not valid. ?? > > Sincerely yours, > Nazanin > ? > > ------------------------------ Message: 20 Date: Wed, 18 Jan 2017 15:56:50 +0000 From: Sneha Pandya <[email protected]> Subject: [Freesurfer] mris_make_surfaces error with bbr-init-header To: Freesurfer <[email protected]> Message-ID: <bn6pr06mb29141f07ea765b590a7aa3adfb...@bn6pr06mb2914.namprd06.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hi all, I have successfully ran recon-all on my subjects with multiple T1s. We want to use flair to refine pial surfaces as for all the subjects pial surfaces are messy and will demand lots of control point edits. After successfully running entire recon-all stream I am running following command to incorporate flair: recon-all -autorecon3 \ -s SUBJ \ -bbr-init-header \ -FLAIRpial \ -bigventricles \ -openmp 12 \ -qcache When I run above command recon-all exits while implementing mris_make_surfaces with an error "Cannot allocate memory" Can someone guide what is happening? Is it that there are large topological error or bbr-init-header flag will only run if I run recon-all from autorecon1 to autorecon3 stage? Thanks, Sneha -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170118/e59e67be/attachment-0001.html ------------------------------ Message: 21 Date: Wed, 18 Jan 2017 11:09:36 -0500 (EST) From: Bruce Fischl <[email protected]> Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header To: Freesurfer support list <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" Hi Sneha how much RAM do you have in your machine? And what is the resolution of your data? cheers Bruce On Wed, 18 Jan 2017, Sneha Pandya wrote: > > Hi all, > > > I have successfully ran recon-all on my subjects with multiple T1s. We want > to use flair to refine pial surfaces as for all the subjects pial surfaces > are messy and will demand lots of control point edits. > > ? > > After successfully running entire recon-all stream I am running following > command to incorporate flair: > > > recon-all -autorecon3 \ > ?? ??? ?-s SUBJ \ > ?? ??? ?-bbr-init-header \ > ?? ??? ?-FLAIRpial \ > ?? ??? ?-bigventricles \ > ?? ??? ?-openmp 12 \ > ?? ??? ?-qcache > > When I run above command recon-all exits while implementing > mris_make_surfaces with an error "Cannot allocate memory" > > Can someone guide what is happening? Is it that there are large topological > error or bbr-init-header flag will only run if I run recon-all from > autorecon1 to?autorecon3 stage? > > Thanks, > > Sneha > > > > ------------------------------ Message: 22 Date: Wed, 18 Jan 2017 11:49:23 -0500 From: Douglas N Greve <[email protected]> Subject: Re: [Freesurfer] Fwd: QDEC versus Terminal annotation To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=windows-1252; format=flowed That vertex (# 130) is just on the border with cuneus, so technically the information is correct On 01/17/2017 11:29 AM, Martin Juneja wrote: > Hi FreeSurfer community, > > I am sorry for reposting the following questions in the discussion forum: > > ---------- Forwarded message ---------- > From: *Martin Juneja* <[email protected] <mailto:[email protected]>> > Date: Fri, Jan 13, 2017 at 4:56 PM > Subject: QDEC versus Terminal annotation > To: Freesurfer support list <[email protected] > <mailto:[email protected]>> > > > Hi, > > I am comparing cortical thickness measures between controls and > patients. I displayed the results in qdec. I found that cluster is > showing significant difference in thickness between controls and > patients (controls having more thickness than patients). > > In terminal, its showing output as: > > ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation > > 1 2.6021 130 1285.86 11.5 -89.5 21.1 1764 > superiorparietal > > I am not an expert in anatomy but when looking at the cluster in qdec > (please find it attached), it seems like the cluster is not superior > parietal as shown in terminal and even TAL coordinates are not > matching with standard superior parietal lobe coordinates. When I > click on find cluster in qdec, shouldn't cursor on that cluster show > the same area shown in terminal? > > Could you please share your thoughts on this, why the area displayed > in terminal window is not matching with the one shown in qdec ? > > Thanks. > > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 155, Issue 27 ******************************************* _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
