Re: [Freesurfer] Desikian-Killiany and Destrieux atlas
For Destrieux atlas labels I think you may use Fig.1 and Tab.1 of the paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/ cheers, giuseppe On 08/11/2018 19:25, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Thank you very much Giuseppe, it's costing me more to find an image similar to the one you send me but with the Destrieux atlas labels. In any case thank you very much for your help, it is what I was looking for. Cheers, El jue., 8 nov. 2018 a las 18:30, Giuseppe Cabras (mailto:giuseppe.cab...@uniud.it>>) escribió: I use the attached legends for FS DK atlas labels. Cheers, g On 08/11/2018 00:47, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Sorry for my unclear question. I only need a brain image that contains the labels of each of the Desikian-Killiany and also Destrieux atlas. This image would allow me to point out to my colleagues the regions where I obtained significant differences between the control group and the experimental group. It would be something similar to the image I send in attached Thanks in advance, Best, desikanKillianyAtlasKey.jpg El mié., 7 nov. 2018 a las 23:23, Greve, Douglas N.,Ph.D. (mailto:dgr...@mgh.harvard.edu>>) escribió: I'm not sure what you mean. The atlas is distributed with FS. On 11/07/2018 05:09 PM, Miguel Ángel Rivas Fernández wrote: > > External Email - Use Caution > > > Hello Freesurfer devs, > > > Is there available any Desikian-Killiany and Destrieux atlas template > or image downloadable with all brain labels of the atlas? I would to > use this image to show my results in a lab meeting? I would need > somethig similar that the lookup table used in the freeview. > > > Cheers, > > -- > *Miguel Ángel Rivas Fernández* > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Giuseppe Cabras, PhD - Department of Mathematics, Computer Science and Physics InterUniversity Center for Behavioral Neurosciences University of Udine - via delle Scienze, 206 - 33100 UDINE Phone: +39-043255-8212 - Skype: giuseppe.cabras61 URL:http://people.uniud.it/page/giuseppe.cabras BOOK:http://www.amazon.com/Advanced-component-analysis-techniques-decomposition/dp/3639873149 * Sunt namque qui scire volunt eo fine tantum, ut sciant; et turpis curiositas est. Et sunt qui scire volunt, ut sciantur ipsi; et turpis vanitas est. [...] Et sunt item qui scire volunt ut scientiam suam vendant; verbi causa, pro pecunia, pro honoribus: et turpis quaestus est. Sed sunt quoque qui scire volunt, ut aedificent; et charitas est. Et item qui scire volunt, ut aedificentur: et prudentia est. Horum omnium soli ultimi duo non inveniuntur in abusione scientiae, quippe qui ad hoc volunt intelligere ut bene faciant. Denique: Intellectus bonus omnibus facientibus eum. Reliqui omnes audiant: Scienti bonum et non facienti, peccatum est ei. (Bernardus Claraevallensis, XII S.: Sermones super Cantica Canticorum, Sermo XXXVI, III) External Email - Use Caution ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer smime.p7s Description: S/MIME Cryptographic Signature External Email - Use Caution___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Best way to elaborate multiple .nii file for multiple subjects
Hi Ottavio,
you can also install gnu parallel
(https://www.gnu.org/software/parallel/) and run in parallel on all your
cpus with just one parallel command line:
export SUBJECTS_DIR=/home/my/study/fs60/MRIstudy/sMRI/native
cd /home/my/MRIdata/sMRI/native
ls *.nii | parallel --jobs 8 recon-all -all -s {.} -i {}
cheers,
Giuseppe
On 25/06/2018 23:49, Ottavio Morciano wrote:
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Without taskset ? Just open terminal and type recon-all -i x -s y -all
for each subjects?
Il lun 25 giu 2018, 23:43 Douglas N. Greve > ha scritto:
If you have 10 processors and enough memory, then you should run 10
simultaneously (ie, without using -openmp).
On 06/25/2018 05:34 PM, Ottavio Morciano wrote:
>
>
> Hi!I'am a student of medicine in Foggia,Italy.To elaborate a single
> .nii file for a single subjects i use "recon-all -i (name of .nii
> file) -s (name of subjects) -all -openmp 8(i have 8 core)"and to
> finish the work is necessary 8 hours.
>
> Now i want elaborate 10 .nii file for 10 subjects(a file for each
> subject).Is better to open 10 terminal and use the command
recon-all
> in each terminal without -openmp,or with -openmp?Or to use
this,Now i
> open 10 terminal BUT for every terminal i use the command
Taskset to
> assign every terminal to a core of my cpus(2 core is busy with 2
> recon-all)
>
> Wich is the best way to finish the work more rapidly?
>
> Sorry for my bad english and i hope for a reply.Thanks
>
> Morciano Ottavio
>
> MD.Student
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] side effects launching recon-all from matlab system(cmd) call
Thanks Douglas for your reply. I checked in detail the talairach_avi.log files and they show that imgreg_4dfp c executable: $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ are executed in both environment (bash and matlab), but in bash imgreg_4dfp call in turn $Id: fimgreg.f,v 1.1 2007/05/04 22:33:59 nicks Exp $ that show eta,q values in the talairach_avi.log file. Seems to me that, if I call recon-all from matlab, fimgreg code ( which I don't know where it is) is not executed or it don't write results to talairach_avi.log output, but probably talairach avi transform is fine. ... very strange behaviour. Cheers, Giuseppe On 11/09/2017 18:25, Douglas N Greve wrote: The tal_QC_AZS scripts expects the log file to have a specific format, and it looks like something changes when you run it inside matlab. sorry, the only idea I have is that the linux environments might be different in bash vs matlab. On 09/11/2017 08:25 AM, Giuseppe Cabras wrote: Dear freesurfer developers, I call recon-all -all from a matlab script using a system(cmd) which is (apparently) correctly executed, as shown in the recon-all.log (matlab_* attached), i.e.: /usr/local/freesurfer/bin/recon-all -all -cw256 -3T -multistrip -clean-bm -i /home/MRIdata/PUD/31148_MRI_sMRI_400614.nii -s /home/gc/study/recon-all/400614dclass and apparently it run without errors as you can see in the matlab_recon-all.log file, but I get (systematically) a wrong TalAviQA: 0.0 while, if I run the above bash command directly I get a correct: TalAviQA: 0.97713 as shown in the bash_recon-all.log (attached). I guessed that something wrong happened in talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig and the error traced in talairach_avi.log (matlab_* and bash_* attached). In fact matlab_talairach_avi.log is shorter and all imgreg_4dfp end sections are missing which imply that TalAviQA can not be extracted by awk and mritotal transform is performed instead. But really I don't understand why this happens and whether similar issues affects other recon-all subtask using matlab. I double checked this on two linux sistems and with fs version 6.0 and 5.3 ... same results. Thanks in advance for any help, cheers, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Giuseppe Cabras, PhD - Department of Mathematics, Computer Science and Physics InterUniversity Center for Behavioral Neurosciences University of Udine - via delle Scienze, 206 - 33100 UDINE Phone: +39-043255-8212 - Skype: giuseppe.cabras61 URL: http://people.uniud.it/page/giuseppe.cabras BOOK:http://www.amazon.com/Advanced-component-analysis-techniques-decomposition/dp/3639873149 * Sunt namque qui scire volunt eo fine tantum, ut sciant; et turpis curiositas est. Et sunt qui scire volunt, ut sciantur ipsi; et turpis vanitas est. [...] Et sunt item qui scire volunt ut scientiam suam vendant; verbi causa, pro pecunia, pro honoribus: et turpis quaestus est. Sed sunt quoque qui scire volunt, ut aedificent; et charitas est. Et item qui scire volunt, ut aedificentur: et prudentia est. Horum omnium soli ultimi duo non inveniuntur in abusione scientiae, quippe qui ad hoc volunt intelligere ut bene faciant. Denique: Intellectus bonus omnibus facientibus eum. Reliqui omnes audiant: Scienti bonum et non facienti, peccatum est ei. (Bernardus Claraevallensis, XII S.: Sermones super Cantica Canticorum, Sermo XXXVI, III) smime.p7s Description: S/MIME Cryptographic Signature ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Talairach transform QA on pre-defaced subjects
Dear FS developers and expert users, I am preprocessing with freesurfer 6.0 recon-all a set of pre defaced subjects and the results are generally good, but the Talairach transform QA measure are terribly bad and exactly the same on all defaced: #- TalAviQA: 0.0 z-score: -222 WARNING: Talairach QA check failed! z-score of -222 is <= threshold of -9 # I have tried a few local subject of the set with face and the QA is acceptable (z-score=-2) and is the same if I pre-deface the subject with mri_deface in FS6.0 with the correct parameters. I don't know how the original datasets were defaced, but I suppose with mri_deface in an unknown older version. I need to process the defaced datasets, but I am warring about the recon-all output measure, in fact I found a thickness error of 28% between deface and face temporal lobe of the same subject. How do you suggest to proceed? Thanks in advance, cheers, Giuseppe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
