[Freesurfer] queue software and routine to remove dura from brain
Hi What kind of queue software is used for Freesurfer to enable multiple instance across several CPU in mulit-core system? Is thesse software available in either Fedora or Ubuntu? I am working with 14 years old image which has enlarged ventricles. What is the recommend setting to remove non-brain tissue like dura from the MRI pictures? Cheers Knut J Bjuland ___ 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] queue software and routine to remove dura from brain
Hi Knut locally we use pbsubmit, but really any queue software should be fine. Do the default settings not work for removing non-brain tissue? Note that as long as the surfaces don't include it it shouldn't matter if it is present in the images. cheers Bruce On Thu, 30 Jun 2011, Knut J Bjuland wrote: Hi What kind of queue software is used for Freesurfer to enable multiple instance across several CPU in mulit-core system? Is thesse software available in either Fedora or Ubuntu? I am working with 14 years old image which has enlarged ventricles. What is the recommend setting to remove non-brain tissue like dura from the MRI pictures? Cheers Knut J Bjuland ___ 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] Cortical Thickness
Hi Freesurfer experts. Do anyone know how to measure the cortical thickness of an specific brain area? I have been using mris_anatomical_stats but it only outputs the brain cortical thickness of the requested hemisphere. Best regards. -- Leo Kay. ___ 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] Cortical Thickness
Hi Leo you can give mris_anatomical_stats a label file with -l, or use -a to get it for each annotation separately cheers Bruce On Thu, 30 Jun 2011, leonardo kay wrote: Hi Freesurfer experts. Do anyone know how to measure the cortical thickness of an specific brain area? I have been using mris_anatomical_stats but it only outputs the brain cortical thickness of the requested hemisphere. Best regards. -- Leo Kay. ___ 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] long_mris_slopes
Hi Sean, symmetrized percent change is a measure across time. for two time points it is just 100*(tp2-tp1)/(0.5*(tp1+tp2)) (if they are a time unit (usually year) apart, else we divide by time difference) You are basically fine. We need to distinguish between processing and post-processing. For processing it makes sense to have 3 time points in the base. You will get a subject template that initializes all time points. This enables you to to a 3time point analysis. It also reduces variability etc. If you run the stream with only two time points in the base for each interval independently you will basically only increase variability of your measures. Of course in post-processing you can look at each interval independently. So looking at the difference in the first interval and in the second separately and then comparing them is totally fine. Also SPC is fine, but: as noted above in SPC we divide by the average . That average of course will change between the intervals and it might be better to divide by the average of all three time points instead (there is no script for that). I don't think it'll make a big difference, though. Alternatively you could look at the difference per time (rate). On the cortex there is so much other variability (noise, non-linear registraton etc). You need to check if what you see is noise or significant. Of course it will go up and down in many regions, but that can all be noise. You should also take a look at the rate, because there you don't divide by the average. And your final question: when looking at spc of all three time points it is NOT the same as viewing only tp1 to tp3. SPC of all three time points is: 100*slope/(temporal average) we fit a line into each subject data and compute the slope (this is the change per time: rate) and divide by the temporal average which is the measure at the mid time. This is assuming there is a linear change Hope that helps. Best, Martin On Jun 28, 2011, at 9:34 AM, Seán Froudist Walsh wrote: Hi Martin and all, I would like to ask you if by comparing tp1 thickness-spc with tp2 (and comparing tp2 with tp3) using the base brain between tp1,2 and 3 (altogether) I have messed up methodologically. I was expecting a rise in cortical thickness in certain areas between tp1 and tp2 followed by a greater rise between tp2 and tp3. I did not expect however a host of other changes which were not seen when viewing spc of tp1, 2 and 3 together. Most of these effects seem to be basically mirror-effects e.g. if there is a rise between tp1 and tp2, there is a drop in thickness in the same area between tp2 and tp3 and vice versa. This happened in several subjects and in variable brain regions. I would like to know if this is because of some methodological flaw. For example, should I run the whole longitudinal stream 2 more times (once to compare tp1 and tp2, and the second time to compare tp2 to tp3)? Also, when viewing the spc of tp1, tp2 and tp3 together are we just looking at the change between timepoints 1 and 3? Many thanks for the help, All the best, Seán On 27 June 2011 11:50, Seán Froudist Walsh froud...@tcd.ie wrote: Hi Martin, That worked! Thanks a lot, Seán On 23 June 2011 18:22, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Sean, I think the --out... names need to be without the ending (mgh) so for example --out-avg=long23.thickness-avg Maybe that'll fix it. Best, Martin On Thu, 2011-06-23 at 09:12 -0700, Seán Froudist Walsh wrote: Dear FreeSurfers, I am looking for a little help comparing longitudinal data. I have three timepoints on each patient and have been able to get individual spc-thickness maps using the long_mris_slopes command where my table included all three time points. I would however like to compare different timepoints with each other: tp3-tp2 and tp2-tp1. I was hoping it would be as simple as specifying a new qdec table including (for example) only tp3 and tp2, and giving new output names using the following command long_mris_slopes --qdec ./qdec/long.qdec.tableTP23.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --out-avg=long23.thickness-avg.mgh --out-rate=long23.thickness-rate.mgh --out-pc1=long23.thickness-pc1.mgh --out-spc=long23.thickness-spc.mgh --out-stack=long23.thickness-stack.mgh --out-label=long23.cortex --time scan --qcache fsaverage but I get the following error: mris_calc: Sorry, but I seem to have encountered an error. While making backup of internal data arrays, it seems that some of the backups already exist. I'm not really sure what the internal data arrays are, and would greatly appreciate any help. Many thanks in advance and all the best, Seán ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] Missing white matter
Hi I have mri picture where there is a large area where white matter is marked as grey. I might also add that this patient has enlarged ventricle and less white matter. I can not send the files on the list, I can however send the files if I get an addresses to send them too. What I ca I say howevere is that in this particulare areas are there none white matter from the cortex to the collusum. Cheers Knut J ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Missing white matter
can you send us a tiff showing the aseg and the cortical surfaces (?h.white and ?h.pial) first? On Thu, 30 Jun 2011, Knut J Bjuland wrote: Hi I have mri picture where there is a large area where white matter is marked as grey. I might also add that this patient has enlarged ventricle and less white matter. I can not send the files on the list, I can however send the files if I get an addresses to send them too. What I ca I say howevere is that in this particulare areas are there none white matter from the cortex to the collusum. Cheers Knut J ___ 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] Trouble downloading freesurfer v4.4
My lab uses freesurfer v4.4, and I'd like to install it on my PC, but the download doesn't seem to be available from the Archives. When I click on any version of the archived file or try to save it to disk, I get a page saying The connection was reset, The connection to the server was rest while the page was loading. Trying to download other releases, such as v5.0 and v4.0.5, produces the same message. The mirror offered for some releases gives me a blank page. Are the files available elsewhere, or will they be put back up at some point? The version I'm looking for is for Mac OS 10.6 (freesurfer-Darwin-leopard-i686-stable-pub-v4.4.0-full.dmg) Thank You, Rachel Steinhorn___ 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] Trac-all: using bvecs/bvals from FSL folder
Hi Jared - We haven't reproduced this error on our end. So if I understand it correctly, replacing bedpostx_seychelles with bedpostx in trac-all would solve the problem? a.y On Wed, 29 Jun 2011, Jared Saletin wrote: Hi Anatasia, Thank you for the response. I've reformatted the files and -prep ran fine. I'm receiving a similar error to some other users upon running -bedp Where bedpostx fails immediately I wanted to point out, and wonder if other folks have had any luck, that if I try running bedpostx from FSL directly on the dmri folder, it starts normally. I can then kill the bedpostx process, and relaunch trac-all -bedp -c ... and things seem to be continuing... It still returns the unexpected operator errors that other users have reported but it does not break to a command prompt anymore, and instead beings return the 0 slices processed ... iterating message. I'm curious, has anyone else had luck navigating around this bedpostx error? Or would it be best to just run bedpostx separately in FSL and return to trac-all after the bedpostx processing is complete? Thanks again! Jared On Jun 28, 2011, at 3:24 PM, Anastasia Yendiki wrote: Hi Jared - Have you looked at $FREESURFER_HOME/bin/dmrirc.example? You can specify bvecfile, bvalfile, and nb0. Currently these are assumed to be the same for all subjects. The format is 3 columns for bvecs, single column for bvals. Otherwise you shouldn't have to do anything else to them (hopefully! :) a.y On Tue, 28 Jun 2011, Jared Saletin wrote: Hi Freesurfer experts, I was wondering if you all had some advice for getting trac-all up and running. I'm trying to work up a trac-all configuration file for a group of subjects, previously processed in FSL. We extracted the Siemens bvec and bval files for the FSL pipeline when importing the dicoms through dicom2nii. I know FSL bval and bvec files are organized in a different matrix shape from what Trac-all wants. Has anyone had sucess with transforming these files? Should/do I need to worry about whether to flip the orientation on bvec files as the images seem to get flipped in the early steps of Trac-all? Also is it possible to feed the configuration file a list of bvec files (for each subject) similar to how we feed it the dicom directory for each subject, or should I create a configuration script for each subject pointing to their bvec file specifically. Thanks in advance for help! Cheers, Jared 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] queue software and routine to remove dura from brain
On Thu, Jun 30, 2011 at 9:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: locally we use pbsubmit, but really any queue software should be fine. Note that pbsubmit is a Martinos-Center wrapper to OpenPBS/Torque Resource Manager. An alternative is Sun^H^H^HOracle Grid Engine (which is also free). Richard ___ 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.
