Freesurfer

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30088 discussions

Siemens Enhanced DICOM
by Funk, Quentin 04 Sep '19

04 Sep '19

External Email - Use Caution Hey all- Freesurfer's recon-all fails if I try to give it a dicom from the new Siemens Enhanced format. Are there any workarounds that don't involve converting to nifti with a different software first? Thanks! Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. houstonmethodist.org | twitter.com/MethodistHosp | facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Scale Option for mris_convert
by rockj5＠netzero.net 04 Sep '19

04 Sep '19

External Email - Use Caution Hello, I normally use mris_convert --combinesurfs for generating STL files from the lh.pial and rh.pial. When running Freesurfer on my local computer, there are no problems with this approach and everything is perfect. However, the lh.pial and rh.pial files I get when running Freesurfer through fMRIPrep are much larger (about 3-4x bigger than the ones I get locally). This makes the STL file I get through mris_convert also much larger. The file size is too big for me to use. I discovered that mris_convert has a scale option using -s. I tried putting -s 0.1, expecting the file size to be reduced 90%. But no matter how little I set the scale to be, the file size is only reduced 1 to 2%. Does anyone know how to properly reduce the STL size using mris_convert? I would really like to avoid having to install a third party software to do this. Thanks a lot! ____________________________________________________________ Beverly Hills Housekeeper Shocks Doctors: Avoid Botox antiaging-breakthrough.com http://thirdpartyoffers.netzero.net/TGL3231/5d700780cb78f7805c97st01duc

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Re: [Freesurfer] recon_all cuda 9.1
by fsbuild 04 Sep '19

04 Sep '19

External Email - Use Caution Hello Vasudev, I think in January of 2018 it was possible to build the development branch of the freesurfer tree using cuda 5.  But I believe that was the last version we tried building the source with.  We no longer support building with cuda and instead favor using OpenMP..  Part of this is because of cuda’s dependencies on the Nvidia graphics hardware which is a moving target.  Some vendors have essentially stopped supporting Nvidia graphics card drivers, e.g., Apple as of Mac OS 10.14 onward.  The Freesurfer dev branch source is now compiled with C++ compilers, and I don’t know that anyone has tried building with cuda since we changed the compilers for freesurfer. - R. On Aug 30, 2019, at 11:39, Dev vasu <vasudevamurthy.devulapally(a)gmail.com> wrote:        External Email - Use Caution        Dear all,Does recon_all -use-gpu only works for CUDA 5.0, is there any way to make it work for CUDA 9.1.ThanksVasudev_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 2

paired t-test for pet surface analysis
by miracle ozzoude 04 Sep '19

04 Sep '19

External Email - Use Caution Hello Freesurfer, I am trying to run a surface based paired ttest for pet. I started by running mri_vol2surf for each pet longitudinal subject. However, when i use mri_concat with --f, --prune, and --paired-diff i get an error " --paired-xxx specified but there are an odd number of frames". I have 4 subjects, 3 has 3 timepoints and 1 has 2 timepoints (total of 11 frames). Below are my commands and full errors. How do I solve this problem? best, Paul *COMMANDS* mri_vol2surf --mov $in_dir/${session}.gtmpvc.output/mgx.ctxgm.nii.gz --reg $in_dir/${session}.gtmpvc.output/aux/bbpet2anat.lta --hemi lh --projfrac 0.5 \ --o $in_dir/lh.mgx.ctxgm.${session}.fsaverage.sm00.nii.gz --cortex --trgsubject fsaverage { echo $in_dir/lh.mgx.ctxgm.${session}.fsaverage.sm00.nii.gz; } >> $lhmgxctx #concatenate the surface pets mri_concat --f "$lhmgxctxgm" --o ${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --prune --paired-diff session=subject_basline.long.baseid (e.g. 001_baseline.long.001, 001_12mon.long.001 etc) lhmgxctx = text file containing the pet volumes mapped to the surface for each timepoints. (e.g. /Analysis/001_baseline.long.001/lh.mgx.ctxgm.001_baseline.long.001.fsaverage.sm00.nii.gz /Analysis/001_12mon.long.001/lh.mgx.ctxgm.001_12mon.long.001.fsaverage.sm00.nii.gz etc.) *ERRORS* + mri_concat --f Analysis/lh_hemi_ctxgm.txt --o Analysis/results/all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --prune --paired-diff-norm1 ninputs = 11 Checking inputs nframestot = 11 ERROR: --paired-xxx specified but there are an odd number of frames

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PALM Analysis
by Harikumar, Amritha 04 Sep '19

04 Sep '19

Hello, Thanks for letting me know regarding running fsPalm in your previous message. My next question is - what command can we use in Freesurfer that can run multiple comparison testing for subcortical regions? If not fsPalm, is there another function that will perform this? Thanks, Amritha Amritha Harikumar Clinical Research Coordinator Holt Emotion and Social Neuroscience Lab Department of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital ___________________________ 149 13th Street, Rm 2620A Charlestown, MA 02129 Phone: 617-724-3283 > On Sep 3, 2019, at 6:06 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > 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 > 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. OHBM International Mentoring Programme Sign-up {Disarmed} > (Meena M. Makary) > 2. PALM Analysis (Harikumar, Amritha) > 3. Re: PALM Analysis (Greve, Douglas N.,Ph.D.) > 4. Discrepancy between thresholded surface and cluster labels > (Bronwyn Overs) > 5. Reconall with no-MPRAGE T1w image? (Rovai Antonin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 Sep 2019 12:19:45 -0400 > From: "Meena M. Makary" <meena.magharious(a)gmail.com> > Subject: [Freesurfer] OHBM International Mentoring Programme Sign-up > {Disarmed} > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CAF4GKtcDD7AdkJFUhQ9KTq_ypOhEo+5Z_Qn+wz6u4kFrvjv=+Q(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi all, > > Between September 1st and September 31st 2019, registration for the fourth > round of the Online International Mentoring Programme organized and > coordinated by the OHBM Student and Postdoc Special Interest Group > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> > will take place. In the programme, every OHBM member can become an (online) > mentor or a mentee to another OHBM member(s) for a period of approximately > one year (October-June). During this time, the mentor can support the > mentee to grow in academia by providing advice on topics such as?but not > limited to?personal development, grant writing, and work-life balance. In > response to the feedback from previous participants and the increased > interest of mentees in industry, we have also invited a number of mentors > from industry to join us for this new round. > > If you are interested in being a mentor and/or mentee, please fill out this > short registration form > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> > and > you will be contacted with further details. > > If you participated in any of the previous rounds and would like to further > take part in the programme, you have two possible ways (It is possible to > choose both options): > > 1. If you would like to continue being paired with your current > mentors/mentees, please first discuss this with your mentoring partner. In > this case, please do not re-subscribe for the programme and please delegate > the mentee to fill in this feedback form > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> > for us. > 2. If you would like to apply for new mentors/mentees, you will be able > to do so using the registration link above. > > Please feel free to forward this message to your colleagues. Please also > forward this email to former researchers working in industry, if you know > any, as we are still looking for more industry representatives to join the > programme as mentors this year. > > We would like to thank all the OHBM mentors and mentees who participated in > the previous three rounds of the programme! The third round of the > programme is now ending. We hope that most of you had an opportunity to > meet in person during the OHBM Annual Meeting in Rome. If you have feedback > for us, please contact us at ohbmtrainees(a)gmail.com > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…>. > Please share any comments which might help to further improve our > programme! > > > To find out more about the programme, please visit the OHBM Student and > Postdoc SIG website > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> > and check our previous publication > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…>. > If you have any questions about the programme, please contact us at > ohbmtrainees(a)gmail.com > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> > . > > > We hope to welcome you in the programme very soon! > > Best regards, > ? > *Meena M. Makary, Ph.D.* > Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/> > Postdoctoral Fellow | Radiology, Harvard Medical School > <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550> > Postdoctoral Fellow | Athinoula A. Martinos Center, MGH > <https://www.nmr.mgh.harvard.edu/user/4550386> > Career Development and Mentoring Manager | OHBM Student and Postdoc SIG > <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449> >

2 1

FreeView : Tools : Volume Filter : Close
by Yasir Hadi 04 Sep '19

04 Sep '19

External Email - Use Caution Hello FreeSurfer Developers, I just want to get the Information: which parameters are used as I apply the filter *Close* on the volume dataset using the FreeView Version 2.0 Builed Jan 18 2017 16:48:55. I've searched the list and the wiki and I didn't find a similar information. Thanks :) Regards, Ysr H

3 2

Re: [Freesurfer] PETsurf kinetic modeling with MRTM
by Chanmi Kim 04 Sep '19

04 Sep '19

External Email - Use Caution Hi Douglas, I checked dicom headers by using ‘dicom_hinfo’ command to get the information of the acquisition time that each frame was acquired. dicom_hinfo -tag 0008,0032 *.dcm Here is the information of the acquisition times: 16:40:08 16:45:08 16:50:08 16:55:08 17:00:08 17:05:08 The number of slices is 90 in each tau PET data, so each dicom file has been acquired at one of the acquisition times. (ex: ADNI3_tau_001.dcm 16:40:08, ADNI3_tau_002.dcm 16:50:08, ADNI3_tau_003.dcm 16:40:08, ... ADNI3_tau_90.dcm 17:00:08) ADNI3 dyamic PET has made up with 6 frames, and each frames took 5 min. So, I think that I can create ‘time.dat’ as below: 164008 164508 165008 165508 170008 170508 Do I use this information? Or should I change anything for making the ‘ time.dat’? Thank you, Chan ------------------------------ Message: 3 Date: Fri, 30 Aug 2019 16:27:03 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] PETsurf kinetic modeling with MRTM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <de737572-1fb1-4bc8-1564-2e80e3c1ced0(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" This is the time at which each frame was acquired. It is just a list of times in seconds in a text file. You will have to go to the person who collected the data On 8/30/2019 10:25 AM, Chanmi Kim wrote: External Email - Use Caution Hello, I'd like to perform MRTM2 approach in ADNI3 tau PET data for partial volume correction (PVC). So, I've tried to do a command line as below. mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz The 'mri_glmfit' required 'time.dat' which is an information of the time activity curve (TAC), however, I don't know how to get this information. Can you please let me know how to get this information? Please share any examples of 'time.dat' If there is anyone who has experience in PetSurf PVC, Chan _______________________________________________

1 0

Compare vertexwise correlation maps
by Matthieu VANHOUTTE 04 Sep '19

04 Sep '19

External Email - Use Caution Dear experts, I would like now to determine if there is statistically difference between vertexwise correlation maps (whether one is statistically "stronger" than the other). Would there be a way to do this with Freesurfer? (r-to-z Fisher transformation and statistical method?) Best regards, Matthieu

3 3

Clusterwise correction for multiple comparisons
by Gwang-Won Kim 04 Sep '19

04 Sep '19

2 1

-conform option in mri_convert produces crazy artefacts
by Rovai Antonin 04 Sep '19

04 Sep '19

External Email - Use Caution Hello again I have the following issue when running mri_convert. When using the option -conform option (as in the reconall pipeline), the sag slices seems to be shifted at some point (see attached pictures). What is happening? By the way the option description is not super clear, could you please give some extra details? Best Antonin [cid:6517702D-5283-43A2-9829-E5FA475ABA23@erasme.ulb.ac.be][cid:BD0A0CE3-A403-4733-9BDC-B38AEED75225@erasme.ulb.ac.be] [Hôpital Erasme] Lien vers Disclaimer<http://www.erasme.ulb.ac.be/email-disclaimer>

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