Freesurfer December 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
131 discussions

Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC {Disarmed}
by Donatienne Van Weehaeghe 07 Dec '20

07 Dec '20

External Email - Use Caution Dear, We also noticed a bad segmentation in another subject in the frontal cortex (see attached figure) which was correctly done using CAT12. Can we change some parameters to fix this? Thank you Kind regards Donatienne [image: image.png] Op do 19 nov. 2020 om 14:33 schreef Donatienne Van Weehaeghe < donatiennevanweehaeghe(a)gmail.com>: > [image: HD_CAU_T1_MR.JPG] > Dear, > > In the attachment the figures.The surface placement is ok. The cautate is > smaller than the segmentation. > > Kind regards > Donatienne > > > > Op wo 11 nov. 2020 om 17:01 schreef Douglas N. Greve < > dgreve(a)mgh.harvard.edu>: > >> The caudate segmentation would not affect the surface placement. Is the >> surface placement ok? Can you send a pic of the caudate error? >> >> On 11/6/2020 9:58 AM, Donatienne Van Weehaeghe wrote: >> >> External Email - Use Caution >> Dear, >> >> Would there be another option to fix this? >> >> Kind regards >> Donatienne >> >> >> Op do 5 nov. 2020 om 17:38 schreef Donatienne Van Weehaeghe < >> donatiennevanweehaeghe(a)gmail.com>: >> >>> The subcortical structures were not delineated correctly, especially the >>> nucleus caudatus which had a lot of atrophy in this particular patient >>> group. >>> >>> Kind regards >>> Donatienne >>> >>> Op do 5 nov. 2020 om 15:50 schreef Douglas N. Greve < >>> dgreve(a)mgh.harvard.edu>: >>> >>>> I don't think CAT creates white or pial surfaces, so no. What is wrong >>>> with your FS analysis? >>>> >>>> On 11/5/2020 2:15 AM, Donatienne Van Weehaeghe wrote: >>>> >>>> External Email - Use Caution >>>> Dear, >>>> >>>> The segmentation using Freesurfer was incorrect, however we have a good >>>> segmentation from Cat 12. Can we use this segmentation for PVC in PETsurfer? >>>> >>>> Kind regards >>>> Donatienne >>>> >>>> _______________________________________________ >>>> Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1ttucMrkcVf3tolfGzKkIhzimsDsR0s6ReyxJTcapE2hY9… <https://secure-web.cisco.com/1ZxmEs2Pk3BSMewoFlR47-yhqcFOo6DC4cKshyj4rTlsuL…> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> *MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/1ttucMrkcVf3tolfGzKkIhzimsDsR0s6ReyxJTcapE2hY9… >>>> <https://secure-web.cisco.com/1ZxmEs2Pk3BSMewoFlR47-yhqcFOo6DC4cKshyj4rTlsuL…> >>> >>> >> _______________________________________________ >> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1ttucMrkcVf3tolfGzKkIhzimsDsR0s6ReyxJTcapE2hY9… > >

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PVE correction tool Petsurfer {Disarmed}
by Julie Ottoy 07 Dec '20

07 Dec '20

External Email - Use Caution Dear FreeSurfer Team, I am interested in the answer to the question of Subin below. I don't think this question was answered -- at least I cannot find the reply. If the PET images are already smoothed to 8mm (which is the case with the post-processed ADNI images), does it make any sense to apply PVC with --psf 8 at all on them? The issue is that ADNI data does not provide the PSF of their scanner/recon method. As such, I am unsure what to do in this case. Thank you for your help! Best regards Julie Re: [Freesurfer] PVE correction tool on Freesurfer 6 <https://secure-web.cisco.com/1nedP2Apnw1D3KcGvp-zqKHEYkSopg1H6QVCkkk17oHpM3…> Lee Subin Kristine <https://secure-web.cisco.com/1mXLTzu2r41QR6HlFRNtEvHNSVSfe8WLOd5uIUAyc7BZMR…> Wed, 20 Jul 2016 02:29:17 -0700 <https://secure-web.cisco.com/18P1Tw0COZDNEtYcEuJXMAL4GATt842M24L2wvu-V1JVmn…> Hi Doug, Thanks for your help! For your response to question #1 from my previous email(copied below), then if all PET images were smoothed so that they all have a uniform resolution of 8mm FWHM, would I put 8 for the psf flag? > 1)*mri_gtmpvc --i pet.nii.gz --reg template.reg.lta--psf FWHM--seg > gtmseg.mgz **--default-seg-merge --auto-mask PSF .01--mgx .01--o > gtmpvc.output * > > (a) For the psf flag, do I have to know exactly the FWHM of the > point-spread function of the scanner or would a default value of 6 > work for all? I am using PET images from multiple centers and thus > each image are from different scanners, and I'm not sure how I would > find the fwhm for each scanner. > In theory you need the FWHM for each scanner. The FWHM can also change depending upon recon method and parameters and even the ligand used. If you get it about right, probably it will be close enough. Also, for the second question (copied below), then does setting it to .01 mean maximum sensitivity to gray matter in each PET voxel, and thus this is the recommended threshold for the most accurate resutls? > (b) For the mgx flag, is the GM threshold .01 an optimal threshold > referring to the p-value?(am new to PVEcorrection and asking out of > curiosity) What is the difference if I enter .01 versus I don't enter it? > You must enter a threshold. When Muller-Gartner is implemented, there are two stages: (1) orthogonalization (subtracting out non-GM) and (2) rescaling. In the rescaling step, each voxel is divided by the fraction of GM in that voxel. If that fraction is 0, then you will get an error. If it is close to 0, you can get extreme noise amplification in that voxel. Setting it to .01 requires that a voxel have at least 1% GM to be rescaled, otherwise the voxel is set to 0. Best, Subin ________________________________ 보낸 사람: Douglas Greve <gr...(a)nmr.mgh.harvard.edu> 대신 freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> 보낸 날짜: 2016년 7월 19일 화요일 오전 10:28:42 받는 사람: freesurfer(a)nmr.mgh.harvard.edu 제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6 the response is in the body f the mail On 7/18/16 9:27 PM, Lee Subin Kristine wrote: Hi Doug, It seems that the email reply you just sent to me was empty. Could you please check your email message again? Thank you as always, Subin ________________________________ 보낸 사람: Douglas N Greve <gr...(a)nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu <gr...(a)nmr.mgh.harvard.edu>> 대신 freesurfer-boun...(a)nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu>> <freesurfer-boun...(a)nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu>> 보낸 날짜: 2016년 7월 19일 화요일 오전 1:59:46 받는 사람: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>> 제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6 On 07/12/2016 11:03 PM, Lee Subin Kristine wrote: > > Hi Doug, > > > Thanks a lot for the page! It was very helpful. > > > I have a few questions about one of the commands and a question for > one of the output files. > > > 1)*mri_gtmpvc --i pet.nii.gz --reg template.reg.lta--psf FWHM--seg > gtmseg.mgz **--default-seg-merge --auto-mask PSF .01--mgx .01--o > gtmpvc.output * > > (a) For the psf flag, do I have to know exactly the FWHM of the > point-spread function of the scanner or would a default value of 6 > work for all? I am using PET images from multiple centers and thus > each image are from different scanners, and I'm not sure how I would > find the fwhm for each scanner. > In theory you need the FWHM for each scanner. The FWHM can also change depending upon recon method and parameters and even the ligand used. If you get it about right, probably it will be close enough. > > (b) For the mgx flag, is the GM threshold .01 an optimal threshold > referring to the p-value?(am new to PVEcorrection and asking out of > curiosity) What is the difference if I enter .01 versus I don't enter it? > You must enter a threshold. When Muller-Gartner is implemented, there are two stages: (1) orthogonalization (subtracting out non-GM) and (2) rescaling. In the rescaling step, each voxel is divided by the fraction of GM in that voxel. If that fraction is 0, then you will get an error. If it is close to 0, you can get extreme noise amplification in that voxel. Setting it to .01 requires that a voxel have at least 1% GM to be rescaled, otherwise the voxel is set to 0. > > > 2) From the *gtm.stats.dat *output file, the 5th column(number of PET > voxels in the ROI) of, for example, the ctx-lh-precuneus and > ctx-rh-precuneus are 1744 and 1805 respectively. However, in the > *?h.aparc.stats* files from recon-all, the 4th column(gray matter > volume) of lh-precuneus and rh-precuneus are 5928 and 6125 > respectively. I am confused because I thought the number of PET voxels > should be equal to the number of GM voxels in the ROI? > You need to scale by the size of the PET voxel. > > Also, for output files such as gtm.nii.gz or nopvc.nii.gz, what > programs can I open them with? It doesn't seem it is openned with > mricron or gedit. > They are nifti files, though you probably don't want to use a nifit viewer. You can load them into matlab with MRIread('file.nii.gz') > > Thank you again in adavnce for your help. > > > Best, > > Subin > > ------------------------------------------------------------------------ > *보낸 사람:* Douglas N Greve > <gr...(a)nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu <gr...(a)nmr.mgh.harvard.edu>> 대신 > freesurfer-boun...(a)nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu>> > <freesurfer-boun...(a)nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu>> > *보낸 날짜:* 2016년 7월 8일 금요일 오전 2:53:31 > *받는 사람:* freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>> > *제목:* Re: [Freesurfer] PVE correction tool on Freesurfer 6 > Hi Subin, I just created this page this morning > http://secure-web.cisco.com/1KvigXsuD3hyHKjk92q3dRvB-q8U59p-kTraKO56xGNX44o… > do you want to take a look and see if it answers your questions. As for > #2, yes you still need to run gtmseg. > > On 06/26/2016 07:45 AM, Lee Subin Kristine wrote: > > > > Hello, > > > > I am trying to use PVE correction on preprocessed PET data downloaded > > from the Alzheimer's Disease Neuroimaging Initiative(ADNI) database. > > I have a couple of questions: > > > > > > 1) I am using the co-registered, averaged image of the dynamic images, > > and it seems from your answers here > > > (https://secure-web.cisco.com/1YfE5sw6IqkPaPVgJHa3pvzOwDjKQNrzaGXppR9K3_johe…) > > > > <https://secure-web.cisco.com/1YfE5sw6IqkPaPVgJHa3pvzOwDjKQNrzaGXppR9K3_johe…>that > > > for static PET images, #3~5 will be different. Could you explain how I > > would need to enter the command differently? > > > > 2) I already have segmentations of my MRI images obtained via > > FreeSurfer(v.5.2)'s cortical parcellation. Would I still have to do > > procedure #1 (gtmeseg --s subject) ? I did try using xcerebralseg > > because it seemed from the help command that in my case where I > > already have some FS segmentations that I should use this one: > > > > /You can use your own segmentation or a modified FS segmentation. // > > //It will be easiest if you modify apas+head.mgz to insert your// > > //segmentations. apas+head.mgz is created by gtmseg but you can// > > //create it with // > > / > > /xcerebralseg --s $subject --o $SUBJECTS_DIR/$subject/mri/apas+head.mgz/ > > > > However when I do try I got the following error: > > > > /ERROR: could not open > > > /usr/local/freesurfer/subjects/002_S_4213/stats/002_S_4213/mri/apas+head.stats > > > for writing// > > //Errno: No such file or directory/ > > > > > > > > Thanks a lot in advance, > > > > Regards, > > Subin > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> > > https://secure-web.cisco.com/1XgYpi_r-CnR048XsavHJjzPHx9p0tYXMIV7Y7H_ffgusy… > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...(a)nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu <gr...(a)nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://secure-web.cisco.com/1_fdkPmqeCBhIOzSeJc1aM0GfvGBSdiksv31DTaDE12Ah_… > http://secure-web.cisco.com/18bdKBUK6GqKjjwPrY-9t1PGsv3xDFzzBRwuZ2LiRDI2-6_…<http://secure-web.cisco.com/18bdKBUK6GqKjjwPrY-9t1PGsv3xDFzzBRwuZ2LiRDI2-6_…> > <http://secure-web.cisco.com/18bdKBUK6GqKjjwPrY-9t1PGsv3xDFzzBRwuZ2LiRDI2-6_…> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> > https://secure-web.cisco.com/1XgYpi_r-CnR048XsavHJjzPHx9p0tYXMIV7Y7H_ffgusy… > > > 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://secure-web.cisco.com/1S6VY8d8Px426OjxBxa0iIIrRKJCZjthW3nj9d7-Z-gjWl9… . 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 <Freesurfer(a)nmr.mgh.harvard.edu>> > https://secure-web.cisco.com/1XgYpi_r-CnR048XsavHJjzPHx9p0tYXMIV7Y7H_ffgusy… -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...(a)nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu <gr...(a)nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://secure-web.cisco.com/1o4YCKE-9GLYA1M8_mdE6MVY7x79Yr2HZgtgud-LVBQztO…<http://secure-web.cisco.com/18bdKBUK6GqKjjwPrY-9t1PGsv3xDFzzBRwuZ2LiRDI2-6_…> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>https://secure-web.cisco.com/1XgYpi_r-CnR048XsavHJjzPHx9p0tYXMIV7Y7H_ffgusy… _______________________________________________ Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>https://secure-web.cisco.com/1XgYpi_r-CnR048XsavHJjzPHx9p0tYXMIV7Y7H_ffgusy… _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://http://secure-web.cisco.com/1S6VY8d8Px426OjxBxa0iIIrRKJCZjthW3nj9d… . 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flipped_hemisphere
by Edoardo Pinzuti 07 Dec '20

07 Dec '20

External Email - Use Caution Hi, after performing a segmentation with Freesurfer and making a Bem model it looks that some results are flipped between right and left hemispheres. Is there a way to check that Freesurfer is interpreting correctly the mri ? Thanks

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Extract he value of area and volume in the fsaverage for every subject
by 李梦君 07 Dec '20

07 Dec '20

External Email - Use Caution Dear FreeSurfer Developers: I compared the cortical thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found a statistic difference region in the cortex area and volume after correction. How can I extract the value of cortex area and volume for every subject in the fsaverage with the code of mri_segstats FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS High Sierra. Best wishes Mengjun Li Second Xiangya Hospital Central South University

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segmentHA_T1.sh failing {Disarmed}
by Keith Harenski 04 Dec '20

04 Dec '20

External Email - Use Caution Hello, I am getting a strange message when trying to run the amygdala and hippocampal sementations, even when attempting to run the script on someone who the script previously completed. When it starts, the script immediately displays the following message: > error parsing license file, expected 4 values The license error message further instructs libc requires a newly formatted license so I got a new one. The new one is identical to the original however and it has four entries - my email address, a five digit number, followed by two alphanumeric strings.. The script then seems to start, will run for about 30 seconds or so then stop again with the following message: > Error using segmentSubjectT1_autoEstimateAlveusML (line 533) > Fitting mesh to synthetic image resulted in no deformation ... > T1 hippocampal subfields exited with ERRORS at Thu Dec 3 15:56:32 MST 2020 I get slightly different errors when running on another subject, who like the one above, previously completed. For this subject the license error is more persistent: > error parsing license file, expected 4 values I've attached the hippocampal-subfields-T1.log for the first subject as it contains the full output. Thank you, Keith -- Keith Harenski Mobile MRI Manager Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory The Mind Research Network 1101 Yale Blvd NE Albuquerque, NM 87106-4188 Office (Cell): 505.504.1338 | Fax: 505.272.8002 kharenski(a)mrn.org | http://secure-web.cisco.com/1dteY9vqOnPkmed6Gi9ngcVDCP_LkM_NDWWJ44EjsUH1kpc… | http://secure-web.cisco.com/1IdoCx7NC76tQWgH2bVZIQ__Bemn520Wpm_zpCLpupf-KHJ…

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Re: [Freesurfer] Freesurfer on new Mac (apple silicon-chip)
by fsbuild 04 Dec '20

04 Dec '20

External Email - Use Caution Hello Cali and Vânia, With the exception of some vector instructions and kernel extensions, Intel binaries should run as is under the Rosetta2 compatability environment on Macs with the M1 chip.  I don't know of issues so far with running freesurfer under the Rosetta 2 environment and I've read some reports of applications not incurring any speed penalty even when running under Rosetta 2. https://secure-web.cisco.com/1ztZwGaxIbaO3u_L5C_nvzS3qQTv8nws7c18mlkQXcNqkt… I also have not heard so far of issues with running freesurfer on an Intel Mac upgraded from Catalina to BigSur.  An issue for some people was upgrading their Intel Macs from older versions of MacOS to Catalina where 32 bit binaries can no longer be run.  The same will be true if you skipped upgrading to Catalina and now upgrade to BigSur instead. In the past I have brought an external hard drive into an Apple store and asked someone for permission to hook it up to one of the new Macs to test running software from my external drive.   They've always let me do this as the store machines have their hard disks wiped and restored I think every day in order to update to the latest software (and get rid of whatever people leave on the machines from playing with them).  Just say no to "time machine" asking to use the disk when you plug it in. - R Cali, Ryan Joseph December 4, 2020 at 09:44 Hi Vânia,   Currently, I am running 7.1.1 (the most recent release) on Big Sur without issue. I’m not sure we can speak to the stability when running it on the new Arm chips given they were just released though if you had issues a virtual machine can serve as an alternative.       Cheers,   Ryan Cali, B.Sc. Research Technician II Center for Neurotechnology and Neurorecovery Laboratory for NeuroImaging of Coma and Consciousness (NICC) Massachusetts General Hospital / Neurology RCALI(a)MGH.HARVARD.EDU 978-860-6496     From: freesurfer-bounces@nmr.mgh.harvard..edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> Date: Friday, December 4, 2020 at 3:41 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Freesurfer on new Mac (apple silicon-chip)         External Email - Use Caution         Hi,   I am about to buy a new laptop and I am wondering if freesurfer will be running on the new mac? I mean, Mac OS big sur (with apple silicon chip, where they no longer use an intel processor)..   Many thanks for your advice. Best, Vânia de Aguiar, PhD Assistant Professor in Neurolinguistics University of Groningen Faculty of Arts Oude Kijk in 't Jatstraat 26 Room 1315..0408 9712 EK, Groningen The Netherlands _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/18KhUD9JwX0LhxXq03DYlcWCcFdsECAiWx6EYx0AQPOAyO… Correia de Aguiar, V.M. December 4, 2020 at 03:40         External Email - Use Caution        Hi, I am about to buy a new laptop and I am wondering if freesurfer will be running on the new mac? I mean, Mac OS big sur (with apple silicon chip, where they no longer use an intel processor).. Many thanks for your advice.Best,Vânia de Aguiar, PhD Assistant Professor in Neurolinguistics University of Groningen Faculty of Arts Oude Kijk in 't Jatstraat 26 Room 1315.0408 9712 EK, Groningen The Netherlands _______________________________________________ Freesurfer mailing list Freesurfer@nmr..mgh.harvard.edu https://secure-web.cisco.com/18KhUD9JwX0LhxXq03DYlcWCcFdsECAiWx6EYx0AQPOAyO…

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Re: [Freesurfer] Freesurfer Digest, Vol 202, Issue 7
by Sandoval, Hugo 04 Dec '20

04 Dec '20

External Email - Use Caution a On 12/3/20, 11:32 AM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu> wrote: CAUTION: This email originated from outside of TTUHSC. Do not click links or open attachments unless you recognize the sender and know the content is safe. Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1lo682NvPBGqZEnPBFI0XoYZbnbhxeUfVtx1Z1h0RAnzup… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: flipped_hemisphere (Mora, Jocelyn S.) 2. Re: recon-all issues debugging (Courtney Haswell) 3. Re: mri_watershed error: problem in the COG calcuation (Julia Yang) ---------------------------------------------------------------------- Message: 1 Date: Thu, 3 Dec 2020 17:31:28 +0000 From: "Mora, Jocelyn S." <JSMORA(a)mgh.harvard.edu> Subject: Re: [Freesurfer] flipped_hemisphere To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <DM6PR04MB530884C1EC8958578085FAC19EF20(a)DM6PR04MB5308.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi, If you are interested in checking information on the volume itself, try mri_info. If you would like specific examples for reference, I would recommend using our wiki pages. Cheers, Jocelyn ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Edoardo Pinzuti <edoardo.pinzuti(a)gmail.com> Sent: Thursday, December 3, 2020 10:34 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] flipped_hemisphere External Email - Use Caution Hi, after performing a segmentation with Freesurfer and making a Bem model it looks that some results are flipped between right and left hemispheres. Is there a way to check that Freesurfer is interpreting correctly the mri ? Thanks

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Freesurfer on new Mac (apple silicon-chip)
by Correia de Aguiar, V.M. 04 Dec '20

04 Dec '20

External Email - Use Caution Hi, I am about to buy a new laptop and I am wondering if freesurfer will be running on the new mac? I mean, Mac OS big sur (with apple silicon chip, where they no longer use an intel processor). Many thanks for your advice. Best, Vânia de Aguiar, PhD Assistant Professor in Neurolinguistics University of Groningen Faculty of Arts Oude Kijk in 't Jatstraat 26 Room 1315.0408 9712 EK, Groningen The Netherlands

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Fwd: Longitudinal pipeline
by vittal korann 04 Dec '20

04 Dec '20

External Email - Use Caution Hello FS experts Thank you for your kind response. This is regarding my previous mail. I think we need to talk about the design matrix X first (sorry, I did not look at your xlsx file; I think it's probably better to send simple csv files if at all). I attached longitudinal data in csv format. Besides the covariates that you mention, the matrix needs to contain an intercept, a variable for ?time?, a variable for ?group? (assuming you have a control group also), and a group-by-time interaction term in order to asses differential change over time (again, if you have a control group). I do not have a control group. Right now I have only schizophrenia patients who underwent 2 scans: the first is the baseline and the second one is after 3 months of yoga therapy. Wish to know how can I proceed with my available data. Just to make sure: ?age? should be ?age at baseline? (i.e. constant across time per subject), otherwise, it will be confounded with time. Yes, I used the same across the study. Could you review (and possibly adapt) your design matrix X with respect to which columns it contains, and write it in the reply? I tried but couldn't get there. Looking forward to your response. Thanks, Vittal

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recon-all issues debugging
by Courtney Haswell 03 Dec '20

03 Dec '20

External Email - Use Caution I am trying to debug why all of our T1's are failing Freesurfer recon-all. It seems that most of the files are being created but it isn't getting to the stats steps to output those files. In the recon-all log it does say "recon-all -s 13265 exited with ERRORS." I looked in the recon-all.error file and the only thing in that is "CMD mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix." Would this be the step where the error is happening? I have checked the T1 thoroughly and it is good quality. What is the best way to debug why this is happening with our scans?

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Freesurfer December 2020