Re: [Freesurfer] Output Time
Hi Isaiah sorry but no, there is no easy way to shorten the processing time except to use multiple processors and open MP cheers Bruce On Thu, 28 Aug 2014, Isaiah C. Smith wrote: > Hello Experts, > > I was wondering if there is a way to short time of recon-all; I see that by > using some of the parameters, one can get rid of different outputs. For mne > forward models and inverses is there a recommended list of necessary and > unnecessary outputs? > > Isaiah Smith > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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] problems with tracula pre-processing (bvecs)
Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval? Good luck, Barbara On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors. I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs Let me know if you need any other information. Thanks in advance for your help. ___ 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] Output Time
Hello Experts, I was wondering if there is a way to short time of recon-all; I see that by using some of the parameters, one can get rid of different outputs. For mne forward models and inverses is there a recommended list of necessary and unnecessary outputs? Isaiah Smith ___ 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] Creating ROI
Hi Juan probably the easiest thing to do is to create an empty volume (in e.g. freeview) with the same geometry as one of our conformed ones, Then run through every voxel in matlab and if its Euclidean distance to your specified center is less than 2.5cm set it to 1, otherwise set it to 0. cheers Bruce On Thu, 28 Aug 2014, Diaz Rodriguez, Juan wrote: I am trying to create a spherical ROI mask in the form of a volume file with 2.5 cm radius. I also have to specify the center of the ROI location. What is the best way to accomplish this? I intend to use this to extract freesurfer cortical thickness values for a region-of-interest (ROI) defined in volume space as described in https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness ___ 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] Creating ROI
I am trying to create a spherical ROI mask in the form of a volume file with 2.5 cm radius. I also have to specify the center of the ROI location. What is the best way to accomplish this? I intend to use this to extract freesurfer cortical thickness values for a region-of-interest (ROI) defined in volume space as described in https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness ___ 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] success and failure of wm surfaces in (almost) identical structural image
Hi Vincent I would say yes. If the skull stripping leaves dura in one image and not in the other, then that could cause big differences as the surface deformation grabs it when it is present. cheers Bruce On Tue, 26 Aug 2014, Vincent Beliveau wrote: I've attached ?h.orig.nofix for both recon with and without wm error. They are similar to ?h.orig in the sense that the one from the recon with wm error misclassifies part of dura as wm. Interestingly when looking at ?h.orig.nofix from the recon with error overlayed on brain.finalsurfs.mgz of the recon without error I can see a few voxels in the misclassified dura are removed from brain.finalsurfs, although not all. Could this small difference explain why we see the wm error in one case and not the other? On 26.08.2014 20:24, Douglas N Greve wrote: how about the ?h.orig.nofix On 08/26/2014 10:45 AM, Vincent Beliveau wrote: Dear Sebastian, Attached is the *.orig for both recon (green being the one with wm error and red being the one with error). Unfortunately they are not identical; a section of the dura is misclassified as wm in the red delineation. As mentionned before, both orig.mgz are numerically identical in that area. As I also mentionned before, the recon were ran on the same machine, same os, same binaries. You expressed some confusion as to what were trying to achieve. We want to figure out why, given numerically almost identical inputs, Freesurfer correctly delineates wm in one case but fails in the other. Unfortunately this type of error appears to be systematic in some of our data. Vincent. On 26.08.2014 16:22, Sebastian Moeller wrote: Hi Vincent hi Melanie, please show us the *.orig surfaces on the critical slice. I predict that these will be identical, If so you can ignore everything except brain.finalsurfs.mgz. Are the two versions of this file identical around the area of mis-classified tissue? I predict that there will be a slight difference. Also if you take Vincent’s brain.finalsurf.mgz and put this into Melanie’s recon and redo the generation of the wm surfaces I predict that now Melinie’s version will show the same problem. On Aug 26, 2014, at 16:08 , Melanie Ganz > wrote: Hi Sebastian, I'm afraid that the problem is slightly more complicated. The inputs to recon-all are almost numerically identical (to the 4th decimal); when converted to orig.mgz, all voxels which are not identical (about only 700 of all the 1677216 voxels) vary only by 1 due to rounding. Their distribution is sparse and do not overlap with the white matter errors. Can such a small source of variation give this kind of difference? Ok, Freesurfer uses some random initialization, however as far as I know the seed is not random and set to 1234. We have looked at all the outputs created before wm.mgz (orig,nu,T1,brainmask,norm,nu_noneck,aseg,brain,wm,filled) and the only one showing a differences overlapping the wm errors is filled.mgz; I think the filled.mgz is changed during the generation of the wm surfaces (at least temporarily)... in all the other images the differences are minor. Are you running the analyses on exactly the same machine and get different results or are you using two “identical” computers? I ask as I think there is a paper about the reproducibility of freesurfer reconstructions(http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038234 ) with different freesurfer versions or different hardware/operating systems that might explain a bit of systematic variance. But I guess I still do
Re: [Freesurfer] watershed surface to volume rendering
Hi Matt you might want to email Matti about this. I think that you can, but he might know the details cheers Bruce On Tue, 26 Aug 2014, Sherwood, Matt wrote: Freesurfer, We have scans that have recon-all completed. Following recon-all, we completed watershed (under the MNE toolbox) to extract skull and scalp from the T1 scans. The outputs of this algorithm are outer brain, inner skull, outer skull and outer scalp surfaces. We are particularly interested in these volumes for our study. Is there a way to convert these surface to volumes representative of CSF (layer between brain/skull), skull (inner to outer skull surface) and skin (outer skull to outer scalp)? Matthew Sherwood Medical Research Engineer Wright State Research Institute 4035 Colonel Glenn Hwy. Dayton, OH 45431 PH: 937.705.1025 FAX: 937.705.1095 EMAIL: matt.sherw...@wright.edu ___ 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] mri_preproc
Hi, I couldn't find the documentation for mri_preproc. I know that roughly it resamples multiple subjects' brain images into the same space and then concatenates the vertices, but I want to know details like: Exactly how are the brains resampled? What is the procedure beyond the Talairach affine and spherical registration steps? Individual brain images have different numbers of vertices. Which vertices are chosen overall? How are they chosen? How is correspondence between a single vertex location across all the images established? Is the finite element approximation and vertex selection procedures invariant? Do they yield the same set and location of vertices despite minor variations? Under what conditions are they invariant? After the vertices are obtained how are they concatenated? Are they listed in a particular order and is this order the same for all the brains? How is the order determined? Thanks in advance for your reply, ~Jen ___ 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] freesurfer version vs cvs version
Thanks. I see that the older ones were done on freesurfer 3.0.2. I am assuming there are not many differences between the segmentation process between 3.0.2 and 3.0.3 so I downloaded 3.0.3 because 3.0.2 is no longer available. I set freesurfer_3.0.3 as the default version and started a recon-all for one of my subjects but it gave me the following error: #@# Skull Stripping Wed Aug 27 15:14:38 PDT 2014 /home/mdiwakar/subjects/20039/mri mri_watershed T1.mgz brainmask.auto.mgz mri_watershed: error while loading shared libraries: libstdc++-libc6.2-2.so.3: cannot open shared object file: No such file or directory Linux sequoia 2.6.18-164.el5 #1 SMP Thu Sep 3 03:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Aug 27 15:14:38 PDT 2014 Yum gave me an rpm that is compatible with this missing library and I installed it but recon-all is still throwing the same error. Any ideas what the problem could be? Joel From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH [ni...@nmr.mgh.harvard.edu] Sent: Tuesday, August 26, 2014 4:58 PM To: Freesurfer support list Subject: Re: [Freesurfer] freesurfer version vs cvs version Joel, The 'recon-all.log' file in the 'scripts' directory of the subject should have the version of freesurfer used. Also, the file 'build-stamp.txt' in that same directory will show the version used. N, On Tue, 2014-08-26 at 18:31 +, Joel R Pieper wrote: > Hello, > > I have 80 subjects' MRIs that were segmented in 2009 with a version of > freesurfer that included this (cvs_version $Id: mri_segstats.c,v > 1.11.2.5 2006/04/13 18:57:07 nicks Exp $) in the aseg.stats output. > The other 19 of my subjects segmented in 2013 display this > (cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks > Exp $) in the output. I think this latest version the 19 subjects were > run on is freesurfer 4.4.0 but I'm not sure which freesurfer version > the older segmentations were run on. The volumes I am looking at are > significantly different between the subjects segmented in 2009 and > those segmented in 2013. I would like to remove any bias in my data > due to different software versions. Is there a way to know which > freesurfer version output the older cvs_version so I can download that > and resegment my 19 subjects to remove version bias? This would be > much quicker than running all 100 subjects on the newest freesurfer > version. > > Joel Pieper > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] recon-all -openmp N question
Thanks, Zeke. Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Z K > Sent: Thursday, August 28, 2014 11:17 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all -openmp N question > > Hi Don, > > Support of openmp is determined by the compiler used to build the code. > gcc4.2 and greater support openmp. > > So the centos6 build does support the openmp flag but the centos4 and > centos4_x86_64 version of freesurfer do NOT. We do not yet build on > centos7 but once we do it surely will support openmp. > > -Zeke > > On 08/28/2014 09:14 AM, Krieger, Donald N. wrote: > > The documentation for the 5.2.0 release (2Mar2013) states that -openmp > > works for the CentOS 6 distribution only. > > > > Is this still the case? > > > > Or does it work for CentOS 7 ? any other Linux version ? > > > > Thanks, > > > > Don > > > > Don Krieger, Ph.D. > > > > Department of Neurological Surgery > > > > Universityof Pittsburgh > > > > (412)648-9654 Office > > > > (412)521-4431 Cell/Text > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > 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] recon-all -openmp N question
Hi Don, Support of openmp is determined by the compiler used to build the code. gcc4.2 and greater support openmp. So the centos6 build does support the openmp flag but the centos4 and centos4_x86_64 version of freesurfer do NOT. We do not yet build on centos7 but once we do it surely will support openmp. -Zeke On 08/28/2014 09:14 AM, Krieger, Donald N. wrote: > The documentation for the 5.2.0 release (2Mar2013) states that –openmp > works for the CentOS 6 distribution only. > > Is this still the case? > > Or does it work for CentOS 7 ? any other Linux version ? > > Thanks, > > Don > > Don Krieger, Ph.D. > > Department of Neurological Surgery > > Universityof Pittsburgh > > (412)648-9654 Office > > (412)521-4431 Cell/Text > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ 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] Research Assistant Position at the University of Washington
Research Assistant Position Integrated Brain Imaging Center University of Washington An experienced, independent, and organized individual is sought for a full-time Research Coordinator position working with Natalia Kleinhans, Ph.D., and Katie McLaughlin, Ph.D., at the Integrated Brain Imaging Center at the University of Washington. The individual in this position would assist with data collection and data processing for two neuroimaging studies of children. Principal duties include: 1) assisting with the administration and support of research projects and activities, including participant recruitment, development of surveys and flyers, and programming fMRI tasks; 2) assisting in data collection through active interaction with child participants, including telephone screening interviews, in-person interviews, and fMRI data acquisition; and 3) conducting pre-processing and analysis of MRI, fMRI, DTI, and MRS data. Ability to work in command line operating systems (Linux) and perform basic shell scripting is required. Previous research or clinical experience with children and experience with other programming languages (e.g., python) is preferred. This position would be an excellent fit for applicants interested in obtaining doctoral training in cognitive neuroscience, clinical psychology, or developmental psychology. To find more information and apply, go to the following website: https://uwhires.admin.washington.edu/eng/candidates/default.cfm?szLocationID=88 Enter req # 111826 ___ 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] Research Assistant Position at the University of Washington
Research Assistant Position Integrated Brain Imaging Center University of Washington An experienced, independent, and organized individual is sought for a full-time Research Coordinator position working with Natalia Kleinhans, Ph.D., and Katie McLaughlin, Ph.D., at the Integrated Brain Imaging Center at the University of Washington. The individual in this position would assist with data collection and data processing for two neuroimaging studies of children. Principal duties include: 1) assisting with the administration and support of research projects and activities, including participant recruitment, development of surveys and flyers, and programming fMRI tasks; 2) assisting in data collection through active interaction with child participants, including telephone screening interviews, in-person interviews, and fMRI data acquisition; and 3) conducting pre-processing and analysis of MRI, fMRI, DTI, and MRS data. Ability to work in command line operating systems (Linux) and perform basic shell scripting is required. Previous research or clinical experience with children and experience with other programming languages (e.g., python) is preferred. This position would be an excellent fit for applicants interested in obtaining doctoral training in cognitive neuroscience, clinical psychology, or developmental psychology. ___ 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] recon-all normalization: bias field output
Dear Bruce and Christian, I found the easy way of simply writing 'set cleanup = 0' at the beginning of mri_nu_correct.mni and then I run this command mri_nu_correct.mni --i T2-scic/mri/orig/001.mgz --o nu.mgz --n 2 This way I get all the masks and iterations that were computed. Now I also see that it generates as many folders as there are iterations, ending with nu2_field and nu2_est if there are two iterations. I see more files now and now I am thinking that the last output is nu2_field, which would be the bias field. So this is why I did not divide anything by hand (also because my 001.mgz and the nu.mgz do not have the same image dimensions) and the info about masked-out voxel would be missing in that case. All the best and thanks. Barbara On 28/08/2014 14:46, Bruce Fischl wrote: > Hi Barbara > what exactly did you divide? If you look at the recon-all.log it will > show the exact inputs and outputs of nu_correct. > > cheers > Bruce > > > On Thu, 28 Aug 2014, Barbara Kreilkamp wrote: > >> Dear Christian, >> >> Thanks a bunch for this answer. I ran all the steps you mentioned >> (except for the one where I simply do uncorrected/corrected, as these >> images have different dimensions, it seems nu3 does more than just >> normalization of intensities, but also image cropping). Do you know >> anything about the image cropping? >> >> I ended up with the output nu1_mask and nu1_est and I think the last one >> is the bias field, at least it looks very much like one :). Am I right? >> >> Thanks for your help, >> Barbara >> >> >> On 27/08/2014 22:53, Christian Thode Larsen wrote: >>> Hi Barbara, >>> >>> I'm not aware of any way that you can do it directly by passing >>> arguments to recon-all (some might correct me on that), but it is possible: >>> >>> 1) As N3 models the bias as a multiplicative effect uncorrected = >>> corrected * bias, the simplest way is to divide each voxel of the volume >>> before and after correction, in order to obtain a volume containing the >>> bias. Note that N3 (by default) works within a mask where low-intensity >>> voxels have been thresholded away. These voxels will contain garbage if >>> you divide all voxels in the volume. >>> >>> 2) Somewhat more complicated: you can specify the -keeptmp flag combined >>> with -tmp SOMEDIR/ (remember the trailing slash) to N3, in order to >>> preserve its working files. This requires you to modify the N3 binary >>> call in the mri_nu_correct.mni script. You also need to convert the mnc >>> files from the tmp dir, so that you can work with the volumes. >>> >>> 3) if you do 2), you also get hold of the low-intensity voxel mask that >>> N3 operates within. You can use this to constrain the division mentioned >>> in 1). >>> >>> Best, >>> Christian >>> >>> On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote: Dear all, Is there a way to output the N3's (non-parametric normalization step) output? I am interested in the bias field that was computed to correct the image intensities. Thank you for your help, Barbara ___ 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 >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] selxavg3-sess error
Dear all, I've run selxavg3-sess and I got this error message when it tried to read the fmcsm file (fmc.sm5.DM.lh.nii.gz). Thank you for your help, Francesca shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy> selxavg3-sess -a rtopy.DM.lh -s SUBJ01 Surface data DM lh -- selxavg3-sess logfile is /usr/local/freesurfer/fsfast/MeytalRetinotopy/log/selxavg3-sess-bold-rtopy.DM.lh-140828163352.log -- --- /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01 Thu Aug 28 16:33:53 IDT 2014 anadir = /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 -- --- matlab output No window system found. Java option 'MWT' ignored. Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. Warning: No window system found. Java option 'MWT' ignored. < M A T L A B (R) > Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> sxa3pwd = /usr/local/freesurfer/fsfast/MeytalRetinotopy >> sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.DM.lh -s SUBJ01 >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# SUBJ01 ### /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/fsfast/MeytalRetinotopy/MRIread.m - outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopy Extension format = nii.gz ERROR: cannot determine format of /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5 ERROR: attempting to read /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5 -- ERROR: fast_selxavg3() failed\n ___ 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] recon-all normalization: bias field output
Hi Barbara what exactly did you divide? If you look at the recon-all.log it will show the exact inputs and outputs of nu_correct. cheers Bruce On Thu, 28 Aug 2014, Barbara Kreilkamp wrote: > Dear Christian, > > Thanks a bunch for this answer. I ran all the steps you mentioned > (except for the one where I simply do uncorrected/corrected, as these > images have different dimensions, it seems nu3 does more than just > normalization of intensities, but also image cropping). Do you know > anything about the image cropping? > > I ended up with the output nu1_mask and nu1_est and I think the last one > is the bias field, at least it looks very much like one :). Am I right? > > Thanks for your help, > Barbara > > > On 27/08/2014 22:53, Christian Thode Larsen wrote: >> Hi Barbara, >> >> I'm not aware of any way that you can do it directly by passing >> arguments to recon-all (some might correct me on that), but it is possible: >> >> 1) As N3 models the bias as a multiplicative effect uncorrected = >> corrected * bias, the simplest way is to divide each voxel of the volume >> before and after correction, in order to obtain a volume containing the >> bias. Note that N3 (by default) works within a mask where low-intensity >> voxels have been thresholded away. These voxels will contain garbage if >> you divide all voxels in the volume. >> >> 2) Somewhat more complicated: you can specify the -keeptmp flag combined >> with -tmp SOMEDIR/ (remember the trailing slash) to N3, in order to >> preserve its working files. This requires you to modify the N3 binary >> call in the mri_nu_correct.mni script. You also need to convert the mnc >> files from the tmp dir, so that you can work with the volumes. >> >> 3) if you do 2), you also get hold of the low-intensity voxel mask that >> N3 operates within. You can use this to constrain the division mentioned >> in 1). >> >> Best, >> Christian >> >> On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote: >>> Dear all, >>> >>> Is there a way to output the N3's (non-parametric normalization step) >>> output? >>> I am interested in the bias field that was computed to correct the image >>> intensities. >>> >>> Thank you for your help, >>> Barbara >>> ___ >>> 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 > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all normalization: bias field output
Hi Barbara, you should just be ble to divide the original image by the nu-corrected one to get the estimated bias field. cheers Bruce On Wed, 27 Aug 2014, Barbara Kreilkamp wrote: > Dear all, > > Is there a way to output the N3's (non-parametric normalization step) > output? > I am interested in the bias field that was computed to correct the image > intensities. > > Thank you for your help, > Barbara > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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] questions about mri_make_bem_surfaces
Hi Gamaliel do you mean a skull model? If so, you might check out Matti Hamalainen's MNE package, which is built on top of FreeSurfer surfaces. cheers Bruce On Wed, 27 Aug 2014, gamaliel huerta urrea wrote: Hi I have questions about the use of the function: mri_make_bem_surfaces I need to create a surface from a set of MRIs in DICOM format. I would like if someone could help me. The only reference I have of the function is: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_make_bem_surfaces and does not say much about its use. Any help is welcome. My idea then is to generate a 3D head model fieldtrip toolbox of Matlab. Regards -- Gamaliel Huerta Ingeniería Civil Biomédica Universidad de Valparaíso ___ 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] recon-all -openmp N question
The documentation for the 5.2.0 release (2Mar2013) states that -openmp works for the CentOS 6 distribution only. Is this still the case? Or does it work for CentOS 7 ? any other Linux version ? Thanks, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text ___ 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] recon-all normalization: bias field output
Dear Christian, Thanks a bunch for this answer. I ran all the steps you mentioned (except for the one where I simply do uncorrected/corrected, as these images have different dimensions, it seems nu3 does more than just normalization of intensities, but also image cropping). Do you know anything about the image cropping? I ended up with the output nu1_mask and nu1_est and I think the last one is the bias field, at least it looks very much like one :). Am I right? Thanks for your help, Barbara On 27/08/2014 22:53, Christian Thode Larsen wrote: > Hi Barbara, > > I'm not aware of any way that you can do it directly by passing > arguments to recon-all (some might correct me on that), but it is possible: > > 1) As N3 models the bias as a multiplicative effect uncorrected = > corrected * bias, the simplest way is to divide each voxel of the volume > before and after correction, in order to obtain a volume containing the > bias. Note that N3 (by default) works within a mask where low-intensity > voxels have been thresholded away. These voxels will contain garbage if > you divide all voxels in the volume. > > 2) Somewhat more complicated: you can specify the -keeptmp flag combined > with -tmp SOMEDIR/ (remember the trailing slash) to N3, in order to > preserve its working files. This requires you to modify the N3 binary > call in the mri_nu_correct.mni script. You also need to convert the mnc > files from the tmp dir, so that you can work with the volumes. > > 3) if you do 2), you also get hold of the low-intensity voxel mask that > N3 operates within. You can use this to constrain the division mentioned > in 1). > > Best, > Christian > > On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote: >> Dear all, >> >> Is there a way to output the N3's (non-parametric normalization step) >> output? >> I am interested in the bias field that was computed to correct the image >> intensities. >> >> Thank you for your help, >> Barbara >> ___ >> 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Qdec question
Hello, I still cannot solve this issue. All help will be appreciated. I am running Qdec analysis on about 100 subjects and correcting with FDR. Once I do this I click the "find clusters and go to max" button and Qdec gives me a plot of all the data as well as taking me to the max vertex in the #1 cluster. I want to extract the data from the table so that I can put it in excel and calculate some correlations however I cannot find a way to do so without hovering or clicking on each data point and manually entering the values into excel. As you can imagine this is very tedious when there are 100 subjects and 12 regions that we are looking at. Please let me know if there is an alternative way to export the data into excel or even to a word processing file so that the values can be copied and pasted into excel. Best, Aurash Abrishamchi Research Co Op - NCRI - Massachusetts General Hospital 165 Cambridge Street, Suite 600 Boston, MA 02214 P: 617-726-4284 aabrisham...@mgh.harvard.edu ___ 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] 3dvolreg.afni error during mc-sess
Dear Doug, Finally, I was able to solve the 3dvolreg.afni error problem. I installed the recent AFNI version for Linux and replaced the 3dvolreg file in Freesurfer/bin by the AFNI 3dvolreg.afni of the AFNI software package. After adding the Suffix .afni (the AFNI-3dvolreg file doesn't end with .afni) the mc-sess runs well. Best wishes, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Freitag, 22. August 2014 18:42 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] 3dvolreg.afni error during mc-sess Hmm, that means that 3dvolreg.afni that comes with FS does not run properly on your system. Do you already have a full version of AFNI installed on your system? doug On 08/22/2014 05:00 AM, Milde, Christopher wrote: > Dear Freesurfer Experts, > > I'm struggling with running only motion correction. > After running mktemplate-sess which ran well, the mc-sess terminates > with the following error. > > The terminal otput is attached: > > "3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: > afni_ncerr > ERROR: 3dvolreg.afni" > > Some important comments: > 1.) 3dvolreg.afni is within the bin-folder of Freesurfer > 2.) I use partial-field-of-view EPI > 3.) I run mc-sess und dcm2nii formated DICOM-files (is it a > prerequisite to use unpacksdcmdir)? > > Thank you, for your support!!! > > Greets Christopher > > *TERMINAL OUTPUT:* > > mc-sess -s PM_00031 -d $FSF_DIR -per-run -fstem -outfmt nii.gz > > [christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run > -fstem 20 -outfmt nii.gz > fmt: Undefinierte Variable. > [christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run > -fstem 20 Logfile is > /home/christopher/Desktop/freesurfer/subjects/S1/log/mc-PM_00923-bold. > log > --- > /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923 > RunList: 001 002 004 > --- ** --- > --- Motion Correcting Run 001 --- > --- ** --- sess = PM_00923 Fr > 22. Aug 09:35:07 CEST 2014 > mc-afni2 --i 001/20.nii.gz --t 001/template.nii.gz --o > 001/fmcpr.nii.gz --mcdat 001/fmcpr.mcdat > /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold > mri_info --nframes --o /tmp/mriinfo.19767 001/template.nii.gz log file > is 001/fmcpr.nii.gz.mclog mcdat file is 001/fmcpr.mcdat tmp dir is > 001/tmp.mc-afni2.19767 #@# > /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold > mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz > --nskip 0 --ndrop 0 -odt float > mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz > --nskip 0 --ndrop 0 -odt float > nskip = 0 > ndrop = 0 > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from 001/template.nii.gz... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras > = (0, -0.218143, 0.975917) k_ras = (0, -0.975917, -0.218143) writing > to 001/tmp.mc-afni2.19767/tempvol.nii.gz... > #@# > /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold > mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz -odt > float mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz > -odt float > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from 001/20.nii.gz... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras > = (0, -0.218143, 0.975917) k_ras = (0, -0.975917, -0.218143) writing > to 001/tmp.mc-afni2.19767/invol.nii.gz... > #@# > /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold > 3dvolreg.afni -verbose -dfile 001/fmcpr.mcdat -1Dmatrix_save > 001/fmcpr.mat -base 001/tmp.mc-afni2.19767/tempvol.nii.gz -prefix > 001/tmp.mc-afni2.19767/outvol.nii.gz > 001/tmp.mc-afni2.19767/invol.nii.gz > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: > afni_ncerr > ERROR: 3dvolreg.afni > Ungültiger leerer Befehl. > > > > > > ___ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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 sen
Re: [Freesurfer] Manual editing compared to non-manual editing.
Dear Kasper, I am glad you enjoyed the course. Mikael Agn, a former master student at NRU, did a small study in his master thesis (http://www2.imm.dtu.dk/pubdb/views/publication_details.php?id=6647) in section 5.3 where he investigated manual edits vs. no manual edits on the same sample. I have repeated Mikael's analysis on more datasets at NRU from 3 scanners and saw that the difference was scanner dependent - meaning for one scanner the surface errors were systematic in the same place due to poor image quality, whereas for others it wasn't. If you'd like more details let em know, cheers, Melanie On 28-08-2014 12:54, Kasper Jessen wrote: Hi, Thank you for a good freesurfer course in Copenhagen. After the course i have been wondering if there is available litterature regarding manuel editing versus non-manuel editing? Has any studies investigated the outcome/results from manual editing versus non-manuel editing on the same sample of subjects? Best regards, Kasper Jessen ___ 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. -- Melanie Ganz, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: melanie.g...@nru.dk web: http://melanie.clausundmelanie.de/ ___ 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] Manual editing compared to non-manual editing.
Hi, Thank you for a good freesurfer course in Copenhagen. After the course i have been wondering if there is available litterature regarding manuel editing versus non-manuel editing? Has any studies investigated the outcome/results from manual editing versus non-manuel editing on the same sample of subjects? Best regards, Kasper Jessen ___ 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] Problems with mri_watershed: almost no skull stripping
Hello, I'm having troubles trying to obtain only the brain in T1-weighted RM images that contain metastases. First of all I have converted the DICOM images to mgz with "mri_convert /usr/local/freesurfer/subjects/A0D0C0.dcm /usr/local/freesurfer/subjects/case1.mgz" . Then, I have employed "mri_watershed -atlas /usr/local/freesurfer/subjects/case1.mgz /usr/local/freesurfer/subjects/brainmaskcase1.mgz" but as I see with freeview, I obtain the original images with a really bad or any skull stripping. For example, in one case, the left part is removed a lot and the right is intact. I have lowered the threshold but nothing changes. How could I solve it? I'm working in VirtualBox and I didn't find the ".license" file, so I haven't copied the three lines. Is it necessary? Thank you very much Regards, Úrsula___ 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] Difference between surfcluster and volcluster
Dear all, I run the surfcluster analysis (mri_surfcluster). But the tutorial tells me that there exists also mri_volcluster: Using the outputs from the estimation step and the simulations, mri_surfcluster (or *mri_volcluster*) will create two outputs: the summary file with a table of the clusters it found, and an output surface map of the clusters wth the cluster-wise p-value. The sample mri_surfcluster command is: mri_surfcluster --src lh.gender_age.glmdir/age/sig.mgh \ --csd lh.gender_age.glmdir/csd1-age.csd \ --csd lh.gender_age.glmdir/csd2-age.csd \ --sum lh.gender_age.glmdir/age/sig.cluster.sum \ --ocp lh.gender_age.glmdir/age/sig.cluster.mgh Could you please tell me the difference between surfcluster and volcluster? How do I have to change the preprocessing steps mris_preproc, smoothing (surf2surf), mdi_glmfit and the simulation to get volcluster instead of surfcluster? Thanks in advance! Katharina ___ 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.
