Re: [Freesurfer] Delay
SubCortGrayVol on Mac is 208022 and 296990 on VM, for the same patient.Does the processing time have something to with the results,it varies a lot. On 29 January 2013 19:33, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Chikku, Can you send us your recon-all.log and recon-all.cmd files? I'd like to investigate why it ran so slowly. Nick On Tue, 2013-01-29 at 06:53 +0100, Varghese Chikku wrote: Dear All, I ran a test subject on VM and the process took 20 hrs to complete.But the same images on Mc pro took 58 hours.VM is 8GB and Mpro is 16 GB.I have noticed this delay happening in the past as well,where VM takes 20-24 for a single patient and Mc takes 24-30 for the same.But,this time ,its was so unexpected.Why is this happening?.Which would be more accurate,and does it mean that more time FS take,the better the results? Many thanks Chikku ___ 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 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.
Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned
Hi Doug, It is indeed correct that columns 1 and 17 are highly correlated. However, for another version of the fsgd file, where the corresponding class and covariate values where identical but with other covariates (so leading to the same columns 1 and 17, other columns are different), all went well. So probably some other columns are highly correlated as well. Anyway, what can we do about it? Just leave the offending covariate(s) out? Cheers, Ed Message: 1 Date: Thu, 24 Jan 2013 12:51:23 -0500 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5101749b.4060...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Ed, the problem is that your covariates are highly correlated. Eg, column 1 is nearly identical to column 17. doug On 01/24/2013 06:36 AM, Ed Gronenschild wrote: Hi, Running mri_glmfit ( v5.0.0, Mac OSX10.6) I got he following error message: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.sib_con_cann_aangepast3.thickness.sm0.mgh --fsgd ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/fsgd_sib_con_cann_aangepast3.fsgd dods --glmdir lh.sib_con_cann_aangepast3.dods.sm0.glmdir --surf fsaverage lh --C ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/group_thickness_gender_scan_age_educ_hand_cann.mtx 2. The FSGD file (if using one) 3. And the design matrix above Please find attached the requested files. I noticed that rows 68 and 147 of the matrix Xg.dat are identical, and most probably caused the error. In the fsgd file I see that the correspondig cases indeed have identical values, although they are referring to different data. How to proceed? Cheers, Ed ___ 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.
Re: [Freesurfer] beta
Hi Bruce, What do you mean: no support anymore or no new development? Cheers, Ed On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote: Message: 7 Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] beta To: Colin Reveley reve...@gmail.com Cc: Joshua Lee jki...@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu, Nick Schmansky ni...@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.00.1301211918340.29...@entry.nmr.mgh.harvard.edu Content-Type: text/plain; charset=iso-8859-1 Hi Colin yes, but we simply don't have the person power to do it at the moment. Our FS support grant ends in a month and is not going to get renewed, so it's going to be hard to do anytime soon. sorry Bruce ___ 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.
Re: [Freesurfer] beta
Hi Ed I mean that the grant funding FreeSurfer maintainance didn't get renewed. We certainly will continue support and development, but it does have a substantial negative impact on the engineering we can do, such as getting rid of the 1mm restrictions. cheers Bruce On Wed, 30 Jan 2013, Ed Gronenschild wrote: Hi Bruce, What do you mean: no support anymore or no new development? Cheers, Ed On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote: Message: 7 Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] beta To: Colin Reveley reve...@gmail.com Cc: Joshua Lee jki...@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu, Nick Schmansky ni...@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.00.1301211918340.29...@entry.nmr.mgh.harvard.edu Content-Type: text/plain; charset=iso-8859-1 Hi Colin yes, but we simply don't have the person power to do it at the moment. Our FS support grant ends in a month and is not going to get renewed, so it's going to be hard to do anytime soon. sorry Bruce ___ 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.
Re: [Freesurfer] mean cortical thickness of significant clusters in qdec
Oh, sorry, I thought you said you were using mri_glmfit-sim (which does not have an FDR option). Are you using the FDR in QDEC? If so, it will display the voxel-wise threshold that realizes the FDR threshold. You can then run mri_glmfit-sim --cache threshold sign --cwpvalthresh .99 where threshold is the voxelwise threshold from FDR and sign is either abs (absolute), pos, or neg. Setting cwpvalthresh=.99 tell it to report all clusters doug On 1/30/13 8:09 AM, Richter, Julia wrote: No it is not...or I just do not find it. Might it be that I only get the xxx.y.ocn.dat if I correct for multiple comparisons with Monte Carlo? If yes, is there any possibility that I get this xxx.y.ocn.dat when correcting with FDR? Many thanks, Julia -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Dienstag, 29. Januar 2013 18:46 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in qdec Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not? doug On 01/29/2013 11:03 AM, Richter, Julia wrote: Dear FreeSurfer experts, I did a group analysis in qdec, found several significant clusters and would now like to extract the mean cortical thickness of each significant cluster. I know that I have to run mri_glmfit-sim to do this, but I do not understand which commands I need to get the xxx.y.ocn.dat as output by running mri_glmfit-sim. Any ideas? Any help is appreciated. J Best wishes, Julia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19
Knut, thanks for testing the other two builds and for filing the report. i noticed they had you run valgrind. if you want, i've put a debug build of mri_convert here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ running it in valgrind i think would output source code line numbers of where its going wrong, which would be a big help. Nick On 29. jan. 2013 21:16, Nick Schmansky wrote: does v5.1 work on this system? no does the centos4_x86_64 v5.2 build work? no. I have filed a bug report on https://bugzilla.redhat.com/show_bug.cgi?id=905638 . It might be problem with mri_convert and glibc interaction. Knut J n. On Tue, 2013-01-29 at 20:33 +0100, Knut J Bjuland wrote: Hi Nick I reran dicom import from /usr/local/freesurfer/subject/sample*. I had 24254940 kB free memory but I still got a segmentation error.I used sample data from /usr/local/freesurfer/subject. Do you think it is a glibc bug in Fedora 18. It contain glibc-2.16-28.fc18.x86_64. This error showed up in my dmesg log. [ 175.413292] mri_convert[1350]: segfault at 0 ip 0037e092fbda sp 7fff0a9dc2c8 error 4 in libc-2.16.so[37e080+1ad000] Knutj On 29. jan. 2013 19:47, Nick Schmansky wrote: Knut, I noticed in the log that there was only 284KB of free memory available, which is not enough to run freesurfer, although it would seem like it should be enough to run the mri_convert command. Can you free-up more memory and re-run? Also, I noticed that you're running the Centos6 build, what OS are you running? Fedora 18? Does the v5.2 Centos4 freesurfer build work on that? Nick On Tue, 2013-01-29 at 19:30 +0100, Knut J Bjuland wrote: When I run recon-all using freesurfer 5.2 latest beta it will segment crash. Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/knutjbj/freesurfer/ernie mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz Segmentation fault Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013 For more details, see the log file /home/knutjbj/freesurfer/ernie/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Knut J ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] beta
This news is most unfortunate. We all appreciate the Freesurfer team's work. Freesurfer, and project's like these, provide a substantial multiplier effect to the productivity of the neuroscience community. There should be more funding for these types of neuroscience research infrastructure. - Joshua On Wed, Jan 30, 2013 at 7:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ed I mean that the grant funding FreeSurfer maintainance didn't get renewed. We certainly will continue support and development, but it does have a substantial negative impact on the engineering we can do, such as getting rid of the 1mm restrictions. cheers Bruce On Wed, 30 Jan 2013, Ed Gronenschild wrote: Hi Bruce, What do you mean: no support anymore or no new development? Cheers, Ed On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote: Message: 7 Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] beta To: Colin Reveley reve...@gmail.com Cc: Joshua Lee jki...@ucdavis.edu, freesurf**e...@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu , Nick Schmansky ni...@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.00.**1301211918340.29...@entry.nmr.** mgh.harvard.edualpine.lrh.2.00.1301211918340.29...@entry.nmr.mgh.harvard.edu Content-Type: text/plain; charset=iso-8859-1 Hi Colin yes, but we simply don't have the person power to do it at the moment. Our FS support grant ends in a month and is not going to get renewed, so it's going to be hard to do anytime soon. sorry Bruce ___ 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 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.
Re: [Freesurfer] beta
thanks Joshua I wish study sections agreed with you. We will probably put in another support grant in the next year when I work up the energy to write one (they are quite dull). I'll probably request support letters at that time. cheers Bruce On Wed, 30 Jan 2013, Joshua Lee wrote: This news is most unfortunate. We all appreciate the Freesurfer team's work. Freesurfer, and project's like these, provide a substantial multiplier effect to the productivity of the neuroscience community. There should be more funding for these types of neuroscience research infrastructure. - Joshua On Wed, Jan 30, 2013 at 7:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ed I mean that the grant funding FreeSurfer maintainance didn't get renewed. We certainly will continue support and development, but it does have a substantial negative impact on the engineering we can do, such as getting rid of the 1mm restrictions. cheers Bruce On Wed, 30 Jan 2013, Ed Gronenschild wrote: Hi Bruce, What do you mean: no support anymore or no new development? Cheers, Ed On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote: Message: 7 Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] beta To: Colin Reveley reve...@gmail.com Cc: Joshua Lee jki...@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu, Nick Schmansky ni...@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.00.1301211918340.29...@entry.nmr.mgh.harvard.edu Content-Type: text/plain; charset=iso-8859-1 Hi Colin yes, but we simply don't have the person power to do it at the moment. Our FS support grant ends in a month and is not going to get renewed, so it's going to be hard to do anytime soon. sorry Bruce ___ 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 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] tracula batch processing
Hello Experts, Unfortunately I am currently only able to run tracula on a personal computer, System Version: Mac OS X 10.6.7 (10J869) Kernel Version: Darwin 10.7.0. I have no problem running a single subject on the dmrirc_single subject configuration file. When I try to run several subjects as described in the configuration file on the tracula tutorial page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula it finishes without errors but only the first subject gets processed. Do you have any ideas of what I am doing wrong? cheers, Cat___ 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.
Re: [Freesurfer] tracula batch processing
Hi Cat - What's the runlist variable set to in the configuration file? a.y On Wed, 30 Jan 2013, Cat Chong wrote: Hello Experts, Unfortunately I am currently only able to run tracula on a personal computer, System Version: Mac OS X 10.6.7 (10J869) Kernel Version: Darwin 10.7.0. I have no problem running a single subject on the dmrirc_single subject configuration file. When I try to run several subjects as described in the configuration file on the tracula tutorial page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula it finishes without errors but only the first subject gets processed. Do you have any ideas of what I am doing wrong? cheers, Cat ___ 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] question about MRF
Dear freesurfer experts, I have questions about the MRF in Freesurfer: (1) I have a T1 image and sub-cortical segmentation for it (nifti format). But the segmentation is not perfect and I would like to relabel it using the ICM algorithm as shown in fig.8 in paper: Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl et al., (2002). How can I do this using Freesurfer? (2) If I have several subjects with labels, how can I train the anisotropic nonstationary MRF prior as equation (9) in the same paper? Can I use that MRF prior elsewhere in my own program? Many thanks! Best, Zhennan -- Zhennan Yan Department of Computer Science Rutgers University ___ 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.
Re: [Freesurfer] mris_pmake
Hi Andrew -- First the good news: Indeed, there is a much simpler (and quicker way): mris_pmake --subj subject --hemi hemi --surface surface --mpmProg autodijk --mpmArgs vertexPolar:0 --mpmOverlay euclidean If called with hemi=lh and surface=smoothwm, it will create an output overlay called lh.autodijk.crv. Each index in the overlay will have a value equal to the shortest distance along the edges of the lh.smoothwm from a start (or polar) vertex, in this case 0, to that particular vertex index in the overlay. The whole operation (including reading all the necessary inputs) takes about 10 seconds on a current-ish Linux workstation (with bogoMips -- type cat /proc/cpuinfo and look for bogomips -- of about 5000) Now the bad news: * The version of 'mris_pmake' in FreeSurfer stable (5.1) is horribly old. And broken. For a start, notice that the all the --surface0 --curv0 --curv1 arguments are no longer required. * The 5.1 version of mris_pmake moreover has a bug in the euclidean overlay code that means it won't work. Better news: * This is all fixed in 5.2 and the above command line I gave will work as advertised. * If you can't wait for the new FS, I'm sure we can send you a compiled preview binary of 'mris_pmake' that will work. * I really really need to update the documentation on mris_pmake... I'd really like to have that ready for the 5.2 release. On Tue Jan 29 17:20:05 2013, Andrew Bock wrote: Dear all, I am trying to calculate the distance from a reference vertex to all other vertices in a surface mesh (or ideally to a subset of vertices), moving along the actual surface (e.g. smoothwm). I am able to loop through the pairs of vertices in which I'm interested, using mris_pmake in each loop, but this is quite time consuming. I have tried using '--mpmProg autodijk' as described in the mris_pmake help file, but have been unsuccessful at getting this command to work. The current code I am using for each pair is: mris_pmake --subject subject --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:###,endVertex:### Any suggestions to cut down my processing time, while still calculating along the surface, would be greatly appreciated. Andrew ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ 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.
Re: [Freesurfer] beta
thanks Fidel we will certainly take you up on it in the next submission Bruce On Wed, 30 Jan 2013, Fidel Vila wrote: Sorry to hear about this. If there is anything it can be done at a FS-virtual-community level that could support the funding request, I'd be supportive of it. Fidel On 2013-01-30, at 9:43, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: thanks Joshua I wish study sections agreed with you. We will probably put in another support grant in the next year when I work up the energy to write one (they are quite dull). I'll probably request support letters at that time. cheers Bruce On Wed, 30 Jan 2013, Joshua Lee wrote: This news is most unfortunate. We all appreciate the Freesurfer team's work. Freesurfer, and project's like these, provide a substantial multiplier effect to the productivity of the neuroscience community. There should be more funding for these types of neuroscience research infrastructure. - Joshua On Wed, Jan 30, 2013 at 7:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ed I mean that the grant funding FreeSurfer maintainance didn't get renewed. We certainly will continue support and development, but it does have a substantial negative impact on the engineering we can do, such as getting rid of the 1mm restrictions. cheers Bruce On Wed, 30 Jan 2013, Ed Gronenschild wrote: Hi Bruce, What do you mean: no support anymore or no new development? Cheers, Ed On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote: Message: 7 Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] beta To: Colin Reveley reve...@gmail.com Cc: Joshua Lee jki...@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu, Nick Schmansky ni...@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.00.1301211918340.29...@entry.nmr.mgh.harvard.edu Content-Type: text/plain; charset=iso-8859-1 Hi Colin yes, but we simply don't have the person power to do it at the moment. Our FS support grant ends in a month and is not going to get renewed, so it's going to be hard to do anytime soon. sorry Bruce ___ 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] question about MRF
Hi Zhennan there is an option to mri_ca_label to read in a prior segmentation and iterate the MRF minimization, but unless your labels and conventions are identical to our's it's unlikely to work. You can use mri_ca_train to build the MRF and likelihoods and such if you want. cheers Bruce On Wed, 30 Jan 2013, Zhennan Yan wrote: Dear freesurfer experts, I have questions about the MRF in Freesurfer: (1) I have a T1 image and sub-cortical segmentation for it (nifti format). But the segmentation is not perfect and I would like to relabel it using the ICM algorithm as shown in fig.8 in paper: Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl et al., (2002). How can I do this using Freesurfer? (2) If I have several subjects with labels, how can I train the anisotropic nonstationary MRF prior as equation (9) in the same paper? Can I use that MRF prior elsewhere in my own program? Many thanks! Best, Zhennan ___ 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] tracula longitudinal
Hello Experts, Please forgive another question. I have run 59 people through the recon-all freesurfer longitudinal stream with 2 timepoints (tp1id, tp2id). I want to run these subjects through tracula next, since the same people also received repeated Tensor imaging. To process everybody through tracula, I would use each person's original (cross-sectional) recon-all output and not the template or -long recon-all output, correct? Best regards, Catherine ___ 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.
Re: [Freesurfer] Delay
oh, that's way too big a difference. Something is wrong On Wed, 30 Jan 2013, Varghese Chikku wrote: SubCortGrayVol on Mac is 208022 and 296990 on VM, for the same patient.Does the processing time have something to with the results,it varies a lot. On 29 January 2013 19:33, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Chikku, Can you send us your recon-all.log and recon-all.cmd files? I'd like to investigate why it ran so slowly. Nick On Tue, 2013-01-29 at 06:53 +0100, Varghese Chikku wrote: Dear All, I ran a test subject on VM and the process took 20 hrs to complete.But the same images on Mc pro took 58 hours.VM is 8GB and Mpro is 16 GB.I have noticed this delay happening in the past as well,where VM takes 20-24 for a single patient and Mc takes 24-30 for the same.But,this time ,its was so unexpected.Why is this happening?.Which would be more accurate,and does it mean that more time FS take,the better the results? Many thanks Chikku ___ 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 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.
Re: [Freesurfer] ERROR: aparcstats2table
The options for these 3: GausCurv FoldInd CurvInd do not exist when I use the -h Thanks, Catherine On 1/29/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: yes, use the -m or --meas flags. If you run it with -h, you will get help and examples doug On 01/29/2013 04:12 PM, Nucleos P wrote: Hello again! Thank you for all your help so far. Just one more question now... is there a way to specify these values to be pulled using a script: GausCurv FoldInd CurvInd ...?? Thanks, Catherine On 1/23/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: They must be in a single folder and the $SUBJECTS_DIR env variable must be set to that folder. If you know a little unix, you can set up folders with symbolic links to subjects' true directories. doug On 01/23/2013 02:58 PM, Nucleos P wrote: Thank you for your help Doug! I was trying to specify the path to get to the subjects. Do I have to have all the subjects in a folder called 'subjects'? I know the naming conventions are important. Thanks again, Catherine On Fri, Jan 18, 2013 at 6:31 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: actually, looking at your cmd line more I see that you have slashes (/) in the subject names. The argument to --subjects should just be a list of name. See the help (aparcstats2table -h) for examples. doug On 01/18/2013 04:58 PM, Nucleos P wrote: Hello experts: Can someone please help me understand what I am doing wrong? This is the first time I am trying this command and it will not work... COMMAND: aparcstats2table --subjects /RGS4_31p/rgs0868_raw /RGS4_31p/rgs0871_raw /RGS4_31p/rgs0883_raw/ /RGS4_31p/rgs1194_raw144/ /RGS4_31p/rgs1311a/ /RGS4_31p/rgs1370a/ /RGS4_31p/rgs1383a/ -t RGS4_31p/aparc.volume.rh -m volume --hemi=rh PATH: [/usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats]:pwd /usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats ERROR: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files ERROR: The stats file /RGS4_31p/rgs0868_raw/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thank you, Catherine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tracula longitudinal
Hi Catherine - Yes, for now treat each time point as a different subject for trac-all purposes. (You can pass the time points' recon-all directories either before or after longitudinal processing.) However, there may also be a longitudinal version of tracula coming soon - but you didn't hear this from me... a.y On Wed, 30 Jan 2013, Cat Chong wrote: Hello Experts, Please forgive another question. I have run 59 people through the recon-all freesurfer longitudinal stream with 2 timepoints (tp1id, tp2id). I want to run these subjects through tracula next, since the same people also received repeated Tensor imaging. To process everybody through tracula, I would use each person's original (cross-sectional) recon-all output and not the template or -long recon-all output, correct? Best regards, Catherine ___ 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.
