[Freesurfer] automatically saving images from tksurfer
Hi folks, Is there anyway to get freesurfer to pop up a surface with an overlay from the command line and get it to just save the image to .tiff and die. Im trying to make a movie from 300 frames of surface with overlay. I can do the popping up the image with overlay from command line of course, but don't know how to save and quit automatically. I am trying to get PySurfer running on a mac, i can install it simply on linux, but someone has decided I must suffer through life with a mac and have not managed to get PySurfer running on mac yet. any thought to help appreciated. greg ___ 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] kill tksurfer auto
Hi Bruce directed me to the tcl scripting stuff for tksurfer and so with a combi of tcl and bash I have almost got my machinery working to make my movies. Just one little fly in the ointment, it keeps putting up one after another tksurfer invocation piled on top the last. I have tried killing last tksurfer invocation with kill -9 $! but i have to loop and wait till the saved image appears and then tksurfer is not the past process ... on and on. problem is the little tcl scripting tutorial does not have a command to kill tksurfer after I save the tif must be a completely simple command to do that but googleing I havent seen it. thanks Greg ___ 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] hippocampal subfield segmentations
I heard from Koen a while back that a new improved version was in the works. I have several projects I would be interested in using it for. Any info on timelines for release or a publication ? thank You ___ 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] label to curv .mgh
hello, trying to convert a medial wall label to a curv format .mgh file running mris_convert --label lh.Medial_wall.label lh.white foo.mgh tried a few things but not getting there, what does it want ? thank You ___ 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] large topological defect
im trying something novel with a veryb young brain, i ran freesurfer standard stream and got decent results and then did some manual editing to fix a skull struip problem and reran and now it is detecting a large defect, is there a way i can look at the data to see what topological defect it is finding and where ? greg ___ 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] hippocampal subfields
Hi, just wondering if you have a guesstimate on the ETA of the new atlas ? thanks On 03/03/14, Juan Eugenio Iglesias wrote: > Dear Gabor, > the segmentation benefits to some extent from higher resolution data, > but produces decent estimates of the subfields at 1x1x1. We are working > on a new atlas that will incorporate much more detail, and will more > effectively take advantage of high-resolution images. > Kind regards, > Juan Eugenio Iglesias > > On Mon, 2014-03-03 at 13:49 +0100, Gabor Perlaki wrote: > > Dear all, > > > > > > 1. Which is the suggested resolution for hippocampal subfields > > segmentation with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3 > > and with 1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields > > segmentation really work with 1.0*1.0*1.0 resolution? > > 2. The article "Automated Segmentation of Hippocampal Subfields from > > Ultra-High Resolution In Vivo MRI." suggested on Freesurfer's page > > uses FOV=448. We are unable to set up the matrix to achieve 0.38mm > > resolution using this FOV. Is there any other suggested article to set > > up our measurements? > > > > Thanks, > > > > -- > > Gabor Perlaki > > > > ___ > > 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
[Freesurfer] version 5.3 bug fix
In the release notes for 5.3 i find Stable release version 5.3.0 is a bug fix release to correct the problem with pial and white surface creation affecting thickness and area measures. Is this only related to netative thickness values, which i have never found. I have 150 subjects * 3 timepoints that i ran on a cluster with condor linux and freesurfer version 5.1 i myself inspected time point 1 and did analysis and did not find any unusual problems. i am preparing to do a longitudinal analysis of all 3 timepoints and wondering if i should reprocess and reinspect everything, considering the bug fix and improvements for longitudinal stream. thanks greg ___ 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] applying Yeo atlas to individual brains
problem with surf2surf is it deals with scalar fields ( data ) so don't think that will do it. problem with label2label is that it deals with a single label which has a diferent structure than anot. so a way to do it 1. mri_annotation2label ... to convert the yeo anotation file to individual labels 2. mri_label2label ... to map each label from the fsaverage space to the individual subject space 3. then the function that takes the labels on the individual subject space and makes a .annot of it in indiv. subject space. you will need to supply a colormap table to, don't remember the name ( google freesurfer make annotation file, or something like that) seems like a lot of work but just make a little script and you only need to figure it out once. if any problems i could dig in my notes, i did not find one function to map a .annot in 1one space to a .annot in another. gref On 03/10/14, Thomas Yeo wrote: > Hi Jeff, > > I am a little unsure myself since I usually work with data mapped to > fsaverage space. I think you might want to use mri_surf2surf, since > there's a "--sval-annot" option. It's hard for me to check now because > I am away at a conference. > > Can someone chime in if mri_surf2surf is wrong? > > Thanks, > Thomas > > > > > > On Mon, Mar 10, 2014 at 10:59 AM, Jeff Eriksen wrote: > > What I need are the ?h.Yeo.annot files for the individual subjects, similar > > to the default ?h.aparc.annot and ?h.aparc.2009.annot files. Will > > mri_label2labe give me that directly? > > > > Thanks, > > -Jeff > > > > > > -Original Message- > > From: Bruce Fischl > > [mailto:fis...@nmr.mgh.harvard.edu](javascript:main.compose() > > Sent: Monday, March 10, 2014 9:50 AM > > To: Jeff Eriksen > > Cc: 'freesurfer@nmr.mgh.harvard.edu' > > Subject: Re: [Freesurfer] applying Yeo atlas to individual brains > > > > Hi Jeff > > > > you should be able to use mri_label2label to map the Yeo atlas from > > fsaverage to any subject. > > > > cheers > > Bruce > > On Mon, 10 Mar 2014, Jeff Eriksen wrote: > > > >> > >> Our lab has a need to apply the Yeo atlas to individual brains. As I > >> understand it, Yeo atlas is only currently available for the FSAverage > >> brain. Any plans to incorporate Yeo on to the default FS segmentation, > >> or have it available as an option? > >> > >> > >> > >> -Jeff Eriksen > >> > >> > >> > >> > >> > > > > > > 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] flash v.s. mprage
looking at the docs available it seems that in general flash is prefered but it seems that for cortical thickness studies you may still favor the mprage ? all with good parameter setting of course. thanks in advance for any clarifying comments you may have Greg ___ 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] LGI radius on outer surface ?
Hello Im preparing an LGI(local gyrification index) manuscript and seems i don't know the default radius that is used for the circular region defined on the outer surface that the boundary of is then projected onto the pial surface to get the corresponding pial region ? hope im clear, not the radius of the closing operator. thank you Greg ___ 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] no aseg
so it seems that i ran make_average_volume which does have a --no-aseg flag make_average_subject really just runs 2 other commands make_average_surface and make_average_volume. bruce the reason i did this is that mike was running a `super` average, i.e. the average subject of 2 different syudies, i.e. ave_study1, ave_study2 and he was running make_average_subject --subjects ave_study1 ave_study2 --out superave. we were doing this so we could map labels from one study to another and we were getting an error in the log file from make_average_volume that indicated it was having a problem with the aseg after the make_average_surface had already finished without error. really we could just skip it i think as we are not actually doing anything with the average volume. greg On 06/04/12, Bruce Fischl wrote: > Hi Michael > > a couple of typos. It should be "make_average_subject" (note no "s"), and it > should be --subjects (note the ending "s"). I also don't see a flag named > --no-aseg, which I think is why it's being included as a subject. What are > you trying to do? > > cheers > Bruce > > On Mon, 4 Jun 2012, michael kruepke wrote: > > >Hi all - > >Having a bit of an issue with trying to run a make_average with the flag > >--no-aseg. When written > > > >make_average_subjects --subject subject1 subject2 --no-aseg --out > >superaverage > > > >the propt runs as if --no-aseg and --out superaverage are subjects i wish to > >average in with subjects1 and subject2. This is obviously and issue, hoping > >someone might have an idea of a solution. I have tried moving these flags to > >somewhere else in the prompt seeing if that would solve it, no luck there. > > > >Best- > >Michael > > > >-- > >Michael D. Kruepke > >PhD - University of Illinois at Urbana-Champaign > >BA - Psych - University of Wisconsin-Madison > >mdkrue...@gmail.com > >(262)-483-7449 > > > > > > > > > ___ > 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] Recent paper on FreeSurfer reliability
bottom line is can we trust freesurfer cortical thickness results and a recent paper my group published seems to give very strong positive answer to the question. paper - cortical thinning in psychopathy, it's on the wiki publication list. All of the areas reported overlap with the areas that have been found in a number of other reports of different modalities in psychopathy,but freesurfer found them all in one dataset,recent high quality publication from kings college on psychopathy ( spm-vbm) found all the same areas except bilateral face and hand motor area ( the exact face and hand areas bilaterally that are associated with emotional binding), i would think the chances of getting this by random error are astronomically low!!!). The ```LEFT``` anterior insula and ```LEFT``` caudal anterior cingulate, again exactly the areas that are consistantly nailed in seperate studies of empathy and they are thinned in psychopaths. the spatial specificity ( the ability to look at the surfaces and tell exactly where the differences are is vastly superior in our freesurfer paper. and this is a study with a group that is not grossly sick, so smaller differences would be expected than a neurodegenerative disease for example. only heuristic validation but my studies with freesurfer always find areas that make sense. the exact value of the cortical thickness are not as important it's the statistical differences in a consitantly processed ( same everything, version etc. ) study well done Bruce & company, i know which software i am using for structural analysis, *freesurfer* my 2 cents Greg Kirk University of Wisconsin Madison On 06/20/12, Nick Schmansky wrote: > Peter, > > Thanks for this info. The Mac OS versions compared in the paper were 10.5 > and 10.6 (Leopard and Snow Leopard). One of the major changes between > these two versions was the switch from a 32b kernel to a 64b kernel > (whereas Snow Leopard and Lion both use a 64b kernel). I havent been able > to definitely say that the math libs changed, but it would seem to account > for the differences in Mac OS version results in the paper. A 32b build > of freesurfer (for the Mac) was used in both tests so kernel differences > might not matter but are suspect. > > Nick > > > We run things on an Xgrid cluster that is now a mixture of Macs running > > Snow Leopard (10.6.8) and Lion (10.7.x). We found the results given from > > asegstats2table and aparcstats2table are identical after running 100 > > subjects on both Mac OS X 10.7.4 and 10.6.8 with Freesurfer 5.1. I also > > ran a few subjects on the cluster and on individual computers (not on the > > cluster so to speak) and the results are identical. > > > > Best, > > Peter > > > > > >> Hi, > >> > >> The paper entitled > >> > >> The Effects of FreeSurfer Version, Workstation Type, > >> and Macintosh Operating System Version on Anatomical > >> Volume and Cortical Thickness Measurements, > >> PLoSONE, Vol 7(6), e38234 (2012) > >> > >> may be of interest to all of you. It can be found at: > >> > >> http://dx.plos.org/10.1371/journal.pone.0038234 > >> > >> Cheers, > >> Ed > > > > ___ > > 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
[Freesurfer] cortical surface area related measures
Hi folks, I wanted to make sure i have everything straight w.r.t. the surface area measures. as i see there are 4 ways implemented ( somewhere ) to do cortical surface area analysis. 1. areal expansion 2. Local Gyrification Index 3. direct vertex based true surface area glm, Winkler AM et. al 4. roi based, i.e. based on the surface areas of the parcellation units in lh.aparc.a2009s.stats etc. 1. recent pub, Lisa T. Eyler et. al used the areal expansion method. was this done exactly as would be achived by using the area tab on qdec and setting up a glm ? Dale published surface area specifying some details of implementation but i was not sure if this was exactly what is implemented in qdec ? 2. LGI seems to me this is the ratio of two areas, that of the hull to the area inscribed by projecting the border of the hull onto the grey/white surface. In an e-mail Nick said LGI is a curvature based measure and that confused me a bit. gyrification is of course related to curvature but it seems the quantities actually calculated here are ratios of areas, which gives local info on surface area differences. 3. the winkler stuff is i think not publicly available yet at this time ? 4. straightforward enough not withstanding ICV corrections, etc. any words of clarification before i start trying some analysis on my group ? thank you Greg ___ 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] is skull strip needed
if there is extra skull left after skull stripping but the pial surface is fine ( i.e. the left skull did not get included in the pial surface ) is it nessesary to adjust watershed parameters or manually remove it and reprocess the data set ? I am thinking it is not needed if it is not causing an error in the surface. thanks greg ___ 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] assembling data
a have a bunch of data stored in the subj_id directories of the subjects for convieniance but it is already in the average surface space, but i want to assemble it into one file so i can run the glm. mris_preproc --fsgd subset.fsgd --target subset_average --hemi lh --meas winkler.mgh --out lh.surf.mgh does not work obviously as the subjects # verticies does not agree ERROR: number of vertices in /study5/aa-scratch/UTAH/freesurfer_subjects/AD33112_2/surf/lh.winkler.mgh does not match surface (163842,149346) because it thinks the surf is on the subj_id surface. how can i accomplish ? cheers greg ___ 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] winkler surf data with qdec ?
Hi , I have winkler variety surface area data that is already smoothed and converted to vertex wise data on my average subject. Each subject has a file rh.ico7.fwhm10.mgh, lh... and Doug gave me a way with mri_concat to assemble the data into a single file so i can run command line mri_glmfit type analysis and that worked out fine. I would like if i can to use qdec so our non command line unix oriented postdoc could easily run a lot of models of interest. the LGI page says you can do recon-all -s my_subject_id -qcache -measure pial_lgi and then add a file .Qdecrc with MEASURE1 = pial_lgi but recon-all -qcache will do smoothing and smoothing has already been done by his fancy specially designed method for the surface interpolated data and also my data is in .mgh format and not curv format like thickness or lgi. is there a way i can cook this goose ? thanks greg ___ 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] putamen seg
Hi, tried to use control points to improve the segmentation of the putamen in the difficult area between putamen,claustrum & insula. adding some white matter control points does not seem to insluence the aseg segmentation. control points are set to 110 after reprocessing with recon-all -autorecon2-cp -autorecon3 -subjid 008 ( v5.1), but these same points are still labeled as putamen? also i do see that some white matter filaments have leaked into the putamen, so the mailing list comments that control points would mess it up seems it would be correct ( if it was affecting the putamen seg, which it does not seem to have done at all). so options are manual editing, here ask opinions, the extra tissue added between the putamen&insula it is doing consistently, so taking the unedited volumes, after checking there are no odd other things added or missing might be more unbiased estimate, that volumes after several human raters had selectively removed a few voxels here and there ? any opinions ? thanks greg ___ 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_glmfit-sim fwhm error
run mri_glmfit-sim --glmdir lh.lgi.glmdir --cache 2 pos get cmdline mri_glmfit --y lh.lgi.10.mgh --fsgd lgi.fsgd dods --C CC.mtx --surf subset_average lh --cortex --glmdir lh.lgi.glmdir SURFACE: subset_average lh log file is lh.lgi.glmdir/cache.mri_glmfit-sim.log cd /study5/aa-scratch/UTAH/freesurfer_final /apps/x86_64_sci6/freesurfer-latest/bin/mri_glmfit-sim --glmdir lh.lgi.glmdir --cache 2 pos $Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Tue Jan 8 14:21:47 CST 2013 Linux tick.keck.waisman.wisc.edu 2.6.32-279.11.1.el6.x86_64 #1 SMP Tue Oct 16 11:16:02 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux gkirk setenv SUBJECTS_DIR /study5/aa-scratch/UTAH/freesurfer_final FREESURFER_HOME /apps/x86_64_sci6/freesurfer-latest Original mri_glmfit command line: cmdline mri_glmfit --y lh.lgi.10.mgh --fsgd lgi.fsgd dods --C CC.mtx --surf subset_average lh --cortex --glmdir lh.lgi.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 38.299834 ERROR: cannot find /apps/x86_64_sci6/freesurfer-latest/average/mult-comp-cor/subset_average/lh/cortex/fwhm38/pos/th20/mc-z.csd i ran mri_surf2surf with --fwhm 10 whats the problem here ? thx greg ___ 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] nu_correct problem
Petr why do you keep trying to name your input files something.mgz, when you were in wisconsin i told you the inputs always need to be 001.mgz at this point i think you need to get invited to upload one of your data sets to ugh and see if there is a problem with the data or is it a problem with your computer. Can someone there at martinos invite Petr to upload the dataset and tell him the mechanism for doing this ? On 01/18/13, zach.p...@post.cz wrote: > > > > > I tried on another standar PC (4 core processor) with XP Win recon-all in > VirtualBox (latest edition) running Ubuntu. > > > > I attach file folder with patient brain - first in VirtualBox as described > and then in command line of terminal Ubuntu window: > > sudo mount - vboxsf folder /home/virtualuser/freesurfer/subjects/folder > > > > Then I convert original TrioTim scanner files using mri_convert -it IMA -ot > mgz filename foldername.mgz > > * here is slight problem - recon log shows that mri_convert recognizes itself > that although my brain files are labeled as IMA that they are not old Siemens > files, so that it unpacks them as DICOM and suggests that if it fails I > should run mri_convert as DICOM > > But after all mri_convert succesfully writes foldername.mgz file as a result > of conversion in foldername directory > > > > Ok, then I run recon-all -subjid foldername -autorecon1 -cw256 > > Now -cw256 was suggested in another error run because files do not fit in 256 > matrix > > Recon stops and sayz no 001.mgz files in /mri/orig directory > > So I copy converted foldername.mgz from foldername directory into /mri/orig > directory and rename it to 001.mgz > > *now here is my question: do all people get 001.mgz file the same way as me? > > Then when I run recon-all -subjid foldername -autorecon1 -cw256 it halts with > error at nu_correct as you can see in attached recon-all.log file > > > > Petr ___ 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_vol2vol call problem
Greetings lords of freesurfer! I am having a problem getting a combined cvs warp+bbregister to map an FA volume onto a template. mri_vol2vol --targ 816 --m3z combined_to816_elreg_afteraseg-norm.m3z --noDefM3zPath --reg /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff.bbr.dat --mov /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/dtifit_FA.nii.gz --o test --no-save-reg spits out Using the m3z file as it is; no assumed location. movvol /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/dtifit_FA.nii.gz targvol 816 outvol test regfile /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff.bbr.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Morphing InvertMorph 0 Synth 0 SynthSeed 1362252270 corRead(): can't open file /study5/aa-scratch/TEENEMO/twins_freesurfer/816/COR-.info i know i have not seen a file COR-.info in the top level subject directory in the modern age of the universe. i know i saw this before but my notes from the last time i figured this out got lost in a file system cleanup. can one of you tell me where i went astray ? thank you Greg ___ 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_vol2vol call
Hi I found my old notes ( re my message earlier) I think this is now correct for mapping subject 822 FA onto my template 816, I know the cvs technology is recent, so just asking to make sure there is now a newer/prefered way. mri_vol2vol --targ /study5/aa-scratch/TEENEMO/twins_freesurfer/816/mri/norm.mgz --m3z /study5/aa-scratch/TEENEMO/twins_freesurfer/822/cvs/combined_to816_elreg_afteraseg-norm.m3z --noDefM3zPath --reg /study5/aa-scratch/TEENEMO/twins_tracula/recons/822/dmri/xfms/anatorig2diff.bbr.dat --mov /study5/aa-scratch/TE ENEMO/twins_tracula/recons/822/dmri/dtifit_FA.nii.gz --o /study5/aa-scratch/TEENEMO/twins_freesurfer/822/cvs/FA.mgz --no-save-reg done thanks ___ 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] -hippo-subfields
we have freesurfer set up on our big condor cluster, i asked that the -hippo-subfields be added. they have it set up to run in 3 stages autorecon1 autorecon2 autorecon3 they added the flag to all 3, i think it would only be needed on autorecon3, but don't think it would cause harm, just be ignored in the first 2 ? thanks greg ___ 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] make movies of non eeg/meg temporal data ?
I would like to make a movie of the temporal evolution of data on the cortical surface from something im doing. similar to what mne_make_movie does, but it's not eeg/meg data. is there a way to make and display movies of data in tksurfer or freeview ? or i guess i could `trick` mne and display my data in the mne package viewer ? any ideas on what is the easiest/best way to skin this cat ? thanks Greg ___ 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] Surface Viewer Issue.
i saw this problem on one redhat installation, not on any others, seems something with the X library orientation information and openGL greg On 10/08/14, Jamie Hanson wrote: > Hi Freesurfer List, > > > I had a (hopefully quick) question about surface viewers and data orientation > in tksurfer v. freeview. > > > I processed all my data in freesurfer v5.3.0 (on a linux cluster) and noticed > something odd when I viewed surfaces. For tksurfer, the surfaces were upside > down when I opened them (see attached pic: tksurfer.png); for freeview, the > data looked fine (see attached pic: freeview.png). > > > I believe the orientation of the images is correct (judging by the freeview > axes), but wondered if this was something others had run into? I uploaded an > example subject to the Martinos Center FileDrop (link: > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=9491zcnivqw). > > > Any thoughts are greatly appreciated! Thanks much! > > > Best, > Jamie. > > > > -- > Jamie L. Hanson > Postdoctoral Fellow, Carolina Consortium on Human Development > Duke University > 417 Chapel Drive > Duke West Campus > Sociology-Psychology Building, Room 07A > Durham, NC 27710 > Email: jamielarshan...@gmail.com > Website: http://jamiehanson.org/ ___ 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] unsupported slice timing pattern 5 ?
hi, started working with a new data set to tracula proc. right off the bat it dies on mri_convert with unsupported slice timing pattern 5 if i simply do mri_convert data.nii.gz dwi_orig.nii.gz it dies with same, it's from a siemens 1.5 mobile scanner. somebody else converted this data to .nii. don't really understand what this is ? basically it's just copying a .nii file, what could it be doing with slice timing ? thanks ___ 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] please help, unsupported slice timing
i am trying to run tracula on a large number of subjects, tracula dies quicklyin -prep stage when mri_convert tries to copy/rename the diffusion data, the error actually comes from the data read function. the data is already in .nii format the error is 'unsupported slice timing pattern 5' this is diffusion data that is already in .nii format so the slice timing information is irrelevant, no slice timing correction is done on diffusion data, but the info was obviously encoded in the nifti header. what do i need to do to get this data to load, go edit the .nii header and 'remove' this info. i tried with the fsledithd function and just setting the 5 to 0 does not work, then i just get a 'read error' with no other information. this data is from a 1.5T siemens mobile scanner so the snr will be a little lower and the bval = 800 is lower so it is just the data that could use the helping hand of the spatial priors to find the tracts. i can run 500 of these if i can get this fixed, incarcerated psychopaths so an important data set. thank you Greg ___ 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] gray scale inflated surf rendering prob
send a question that martina asked before and we have not solved the prob. on macs when we run tksurfer xxx lh inflated for example the surf comes up looking smoother,low resolution rendered. if we load something like curvature that displays in color the surface looks fine, so the problem is only with the grayscale surfaces. this occurs on all the macs in a psychiatry dept. lab,other macs at other labs around the surfs always appear normal, i have never seen this problem before, the machines used to display the surfs normally and then all of a sudden it started happening all the time on this one group of macs, seems it must be associated with some config change or upgrade,but i am not much of a mac uses, i use linux. anybody out in freesurfer land seen something like this and can give me a clue ? thanks greg ___ 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] bbregister coordinates
Happy new year folks, i would like to get info on which axis the transformation info in the fregister_XXX.dat.param is w.r.t. comparing the log files with the values i think the first 3 are the translations and the next 3 the rotations. but i did not see w.r.t. which directions, i.e. LR,AP,IS for the 3 translations for the rotations w.r.t. which planes , i.e. 1st rotation LR&AP , 2nd etc. all w.r.t. conformed space, i.e. the directions w.r.t. brain.mgz did i miss a doc. that tells me this thanks Greg ___ 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] cvs register mri_aparc2aseg running 22 hours ?
im running mri_cvs_register --step2, running it in a shell, not in the background. the process returned but top shows mri_aparc2aseg still running at 100% cpu for 1320 minutes. seems something is not running correctly ? greg ___ 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] problem applying morph with mri_vol2vol
Hi i am trying to transform/morph a tract created with tracula into my cvs template subject space, using v.5.0 i am thinking the bb register transformation i am using is not the correct one, but it seems the logical choice, but obviously not working good as forceps minor ends up wraped around the brain stem. here is what i run mri_vol2vol --targ /study5/aa-scratch/TEENEMO/freesurfer_subjects/033/mri/norm.mgz --m3z combined_to033_elreg_afteraseg-norm.m3z --noDefM3zPath --fsl /study5/aa-scratch/TEENEMO/freesurfer_local/toot/006//dmri/xfms/diff2anat.bbr.mat --mov /study5/aa-scratch/TEENEMO/freesurfer_local/toot/006/dpath/fminor_PP_avg33_mni_bbr/path.pd.nii.gz --out ./to033path.pd.nii.gz --interp trilin --no-save-reg thanks greg ___ 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] white matter hyper intensities
a collaborator just got a grant review that claimed There's a possibility that changes in cortical thickness in the insula might be a consequence of lesions (MR-hyperintensities) in the white matter. i would think that white matter hyper intensities would tend to enhance freesurfers ability to detect the white matter/grey matter boundary rather than cause an error. any comments as to the correctness of my thinking would be appreciated. thank you greg ___ 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] white matter hyper intensities
interestingly, in this case i think there may even be reason why white matter hyper intensities could be more common in our insular region of interest where we detected thinning. The disease is HIV and activated monocytes invade the perivascular spaces where they can cause inflamation, which the lit. seems to say can cause white matter hyper intensities. these virchow robin spaces are prominent around the insula and may in fact this may be the etiology of the changes there. so i guess i should try and tease apart which it is, maybe add flair imaging. thanks for the comments greg On 04/05/12, Bruce Fischl wrote: > Hi Greg, > > yes, that can happen where they are hyper-intense on T2 and hypo-intense on > T1 and thus look like GM on the T1. It's not that common since they are > usually deeper, but we have seen it. > > sorry > Bruce > > > On Wed, 4 Apr 2012, Gregory Kirk wrote: > > >a collaborator just got a grant review that claimed > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >There's a possibility that changes in cortical thickness in > >the insula might be a consequence of lesions (MR-hyperintensities) in the > >white > >matter. > > > > > >i would think that white matter hyper intensities would tend to enhance > >freesurfers ability > >to detect the white matter/grey matter boundary rather than cause an error. > > > > > >any comments as to the correctness of my thinking would be appreciated. > > > > > >thank you > > > > > >greg > > > >___ > >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
