Freesurfer August 2012

freesurfer@nmr.mgh.harvard.edu

110 participants
170 discussions

Thresholding using FDR
by Ian Carroll 03 Aug '12

03 Aug '12

Hello, When thresholding significance using FDR for one of my overlays, I noticed that a rate of .1 and .05 give me the same minimum and maximum threshold values. At both levels, there were no voxels of significance. Does this mean that freesurfer will not continue to update max and min values when nothing is significant? Thanks, Ian

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Re: [Freesurfer] Longitudinal cortical thickness analysis
by Martin Reuter 03 Aug '12

03 Aug '12

Hi Venkat, in 5.0 images are not aligned as longitudinal runs are done in their native (cross sectional spaces). since 5.1 we map everything to the base in the initial conform reslicing step to make visualization and debugging easier. this further decreases variability. Although 5.0 does not align the images it should still work. So maybe you have no problem at all. If you rerun, make sure you re-run the base and the longitudinal directories from scratch, not on top of the old ones. About processing stats files, there are several options: 1. grab the measures from the stats files yourself and input them into any statistic package you desire. For this asegstats2table may be helpful (also aparcstats2table). This is recommended as it is most flexible, e.g. you can run linear mixed models, which is better than looking simply at slopes. In your case (only 2 time points) it may not matter much, but linear mixed models can deal with missing data (e.g. if you have subjects with a single time point only). 2. (some quick stuff I implemented for simple analysis, similar to long_mris_slopes) get long_stats_slopes (and all the other files there) from: http://martinos.org/~mreuter/long/ backup yours and replace with these. long_stats_slopes works the same way as long_mris_slopes. You can run the output (e.g. rate/year or percent change) through glm_fit for your group analysis (there is a tutorial about glm_fit). We are working on making available more powerful statistical tools for longitudinal analyses in the future. Then we will also create a better tutorial for it. Best, Martin On Fri, 2012-08-03 at 10:31 -0400, Rajagopalan, Venkateswaran wrote: > Hi Martin, > > Thanks for your immediate response. > > are you using version 5.1 ? > No version 5.0 I am undating it. > After the upgarde I will run the program again and see whether the > same problem persists. > > The most common > reason is that skull strip fails in the cross sectional runs. Large > chunks of skull can throw off the registration in the base. > > I verified my skull strip (I always do) and it is fine in this case. > In your case, you have only 2 time points and an error in the > registration would immediately result in a messed up norm.mgz image in > the base:nonhyper_24_templ/mri/norm.mgz would be very blurry or show > two ghost > images. > > I didn't see base image being messed up in my case though. > > Also I am interested in seeing whether is there any reduction in > cortical thickness between the two time points. In that case how to do > stats. I am unable to find guidelines to do stats after the > longitudinal processing (processing steps for longitudinal is very > good but unfortunately I am unable to find one for stats part). > > Thanks > > Venkat > > > > > > ______________________________________________________________________ > From: Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] > Sent: Thu 8/2/2012 3:37 PM > To: Rajagopalan, Venkateswaran > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Longitudinal cortical thickness analysis > > > Hi Venkat, > > are you using version 5.1 ? In earlier versions, time points were not > aligned to the base, so they don't align. Since 5.1 they should > perfectly align. If not it can have several reasons. The most common > reason is that skull strip fails in the cross sectional runs. Large > chunks of skull can throw off the registration in the base. > > In your case, you have only 2 time points and an error in the > registration would immediately result in a messed up norm.mgz image in > the base: > > nonhyper_24_templ/mri/norm.mgz would be very blurry or show two ghost > images. > > So take a look at that and also the skull strip in > nonhyper_24_06/mri/brainmask.mgz > nonhyper_24_07/mri/brainmask.mgz > > and fix them if it they are bad. > > Best, Martin > > On Thu, 2012-08-02 at 13:48 -0400, Rajagopalan, Venkateswaran wrote: > > > > Dear All, > > > > I ran the following steps in a patient of mine at two time points > > nonhyper_24_06 and nonhyper_24_07 > > > > recon-all -autorecon1 -subjid nonhyper_24_06 > > recon-all -autorecon1 -subjid nonhyper_24_07 > > recon-all -autorecon2 -subjid nonhyper_24_06 > > recon-all -autorecon3 -subjid nonhyper_24_06 > > recon-all -autorecon2 -subjid nonhyper_24_07 > > recon-all -autorecon3 -subjid nonhyper_24_07 > > > > # template creation > > > > recon-all -base nonhyper_24_templ -tp nonhyper_24_06 -tp > > nonhyper_24_07 -all > > > > recon-all -long nonhyper_24_06 nonhyper_24_templ -all > > recon-all -long nonhyper_24_07 nonhyper_24_templ -all > > > > When I tried to inspect my longitudinal result using > > freeview -v nonhyper_24_06.long.nonhyper_24_templ/mri/norm.mgz \ > > nonhyper_24_07.long.nonhyper_24_templ/mri/norm.mgz \ > > -f > > nonhyper_24_06.long.nonhyper_24_templ/surf/lh.pial:edgecolor=red \ > > > > nonhyper_24_06.long.nonhyper_24_templ/surf/lh.white:edgecolor=blue \ > > > > > nonhyper_24_07.long.nonhyper_24_templ/surf/lh.pial:edgecolor=255,128,128 \ > > > > > nonhyper_24_07.long.nonhyper_24_templ/surf/lh.white:edgecolor=lightblue > > > > My norm images from two time points doesn't overlap (so does the > pial > > and white surfaces from two points they appear on two distinct > places > > on the freeview instead of being overlaped as shown in tutorial) > when > > I load then it looks like there is some registration problem. I > don't > > know where I made a mistake and how to correct for this. > > Any help will be greatly appreciated. > > > > Thanks > > Venkat > > > > > > =================================== > > > > > > Please consider the environment before printing this e-mail > > > > Cleveland Clinic is ranked one of the top hospitals in America by > > U.S.News & World Report (2010). Visit us online at > > http://www.clevelandclinic.org for a complete listing of our > services, > > staff and locations. Confidentiality Note: This message is intended > > for use only by the individual or entity to which it is addressed > and > > may contain information that is privileged, confidential, and exempt > > from disclosure under applicable law. If the reader of this message > is > > not the intended recipient or the employee or agent responsible for > > delivering the message to the intended recipient, you are hereby > > notified that any dissemination, distribution or copying of this > > communication is strictly prohibited. If you have received this > > communication in error, please contact the sender immediately and > > destroy the material in its entirety, whether electronic or hard > copy. > > Thank you. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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. > > > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals in America by > U.S.News & World Report (2010). Visit us online at > http://www.clevelandclinic.org for a complete listing of our services, > staff and locations. Confidentiality Note: This message is intended > for use only by the individual or entity to which it is addressed and > may contain information that is privileged, confidential, and exempt > from disclosure under applicable law. If the reader of this message is > not the intended recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are hereby > notified that any dissemination, distribution or copying of this > communication is strictly prohibited. If you have received this > communication in error, please contact the sender immediately and > destroy the material in its entirety, whether electronic or hard copy. > Thank you. > >

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Re: [Freesurfer] expert option error in recon-all
by james pardon 03 Aug '12

03 Aug '12

Hi Bruce, subject's folder is empty, there is no scripts folder, or anything else. Again if I omit -expert everything works fine. Thanks On Fri, Aug 3, 2012 at 7:36 PM, james pardon <james.pardon15(a)gmail.com>wrote: > Hi Bruce, > > subject's folder is empty, there is no scripts folder, or anything else. > Again if I omit -expert everything works fine. > > Thanks > > > On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> Hi James >> >> what happens if you run: >> >> ls -l /home/dir/subject/subname/**scripts/expert-options >> touch /home/dir/subject/subname/**scripts/expert-options >> >> Bruce >> >> >> On Fri, 3 Aug 2012, james pardon wrote: >> >> Dear all, >>> I'm trying to pass the following flags for mri_normalize through -expert >>> flag in recon-all, with a file, named expert.opts with the following >>> single >>> line: >>> mri_normalize -b 20 -n 5 >>> >>> my command line is: >>> >>> recon-all -i inputfile -subject subname -all -expert >>> <pathname>/expert.opts >>> >>> I receive the following error: >>> >>> cp: cannot create regular file: >>> '/home/dir/subject/subname/**scripts/expert-options' >>> >>> The directory of the subject has been created, but it is completely >>> empty. >>> At first glance I thought it might be some sort of permission problems, >>> however I have rwx permission for all the paths (even running under the >>> root >>> username the same error comes up). Secondly, I checked my disk quota, it >>> is >>> completely fine. Please note that, if I do not pass -expert flag >>> recon-all >>> works completely fine. >>> >>> Any input is much appreciated. >>> >>> Regards, >>> James >>> >>> >>> >> >> 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<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. >> > >

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expert option error in recon-all
by james pardon 03 Aug '12

03 Aug '12

Dear all, I'm trying to pass the following flags for mri_normalize through -expert flag in recon-all, with a file, named expert.opts with the following single line: mri_normalize -b 20 -n 5 my command line is: recon-all -i inputfile -subject subname -all -expert <pathname>/expert.opts I receive the following error: cp: cannot create regular file: '/home/dir/subject/subname/scripts/expert-options' The directory of the subject has been created, but it is completely empty. At first glance I thought it might be some sort of permission problems, however I have rwx permission for all the paths (even running under the root username the same error comes up). Secondly, I checked my disk quota, it is completely fine. Please note that, if I do not pass -expert flag recon-all works completely fine. Any input is much appreciated. Regards, James

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Lesion segmentation
by Hunold, Alexander 03 Aug '12

03 Aug '12

Dear Experts, >From my understanding, the segmentation of lesions within the brain tissue is none of your main interests. However earlier threads indicated that there are some tools related to FreeSurfer which could help with such a task. Precisely, I am looking for a way to segment the surface of a lesion in a T1 dataset. I am not afraid of doing the segmentation manually (only 2 participants), but I would prefer receiving an output in FreeSurfer surface format which is coregistered with the regular output, e.g. lh.white, rh.pial, etc. Can you point me to a procedure within FreeSurfer or to a tool associated to FreeSurfer, to fulfill this task? Any hint is appreciated very much. Thanks a lot in advance. Best regards, Alexander Hunold

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FreeSurfer with pediatric brain tumors?
by Jesse Bledsoe 02 Aug '12

02 Aug '12

Hello FS experts, I am wondering if anyone has experience using FreeSurfer or other program to analyze cortical thickness and subcortical volumes in children with pediatric brain tumors? Will adding control points in tumor regions be an adequate intervention for the topological defects? Thought I'd ask for advice before taking the plunge. Best regards, Jesse

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subcortical gray matter volumes
by Fred Sanders 02 Aug '12

02 Aug '12

Hi All, Two questions: 1. I am interested in subcortical gray matter volumes such as hippocampus, amygdala, & basal ganglia. Can someone recommend some good references looking at the accuracy of Freesurfer relative to the "gold standard" approach of hand-tracing these structures? 2. Most of the problems that require quality checks for Freesurfer relate to defining the cortical surface and the grey-white boundary. As far as I can tell, there is rarely a need to edit Freesurfer's definitions of subcortical gray. Am I correct in this? Thanks! Fred

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Longitudinal cortical thickness analysis
by Rajagopalan, Venkateswaran 02 Aug '12

02 Aug '12

Dear All, I ran the following steps in a patient of mine at two time points nonhyper_24_06 and nonhyper_24_07 recon-all -autorecon1 -subjid nonhyper_24_06 recon-all -autorecon1 -subjid nonhyper_24_07 recon-all -autorecon2 -subjid nonhyper_24_06 recon-all -autorecon3 -subjid nonhyper_24_06 recon-all -autorecon2 -subjid nonhyper_24_07 recon-all -autorecon3 -subjid nonhyper_24_07 # template creation recon-all -base nonhyper_24_templ -tp nonhyper_24_06 -tp nonhyper_24_07 -all recon-all -long nonhyper_24_06 nonhyper_24_templ -all recon-all -long nonhyper_24_07 nonhyper_24_templ -all When I tried to inspect my longitudinal result using freeview -v nonhyper_24_06.long.nonhyper_24_templ/mri/norm.mgz \ nonhyper_24_07.long.nonhyper_24_templ/mri/norm.mgz \ -f nonhyper_24_06.long.nonhyper_24_templ/surf/lh.pial:edgecolor=red \ nonhyper_24_06.long.nonhyper_24_templ/surf/lh.white:edgecolor=blue \ nonhyper_24_07.long.nonhyper_24_templ/surf/lh.pial:edgecolor=255,128,128 \ nonhyper_24_07.long.nonhyper_24_templ/surf/lh.white:edgecolor=lightblue My norm images from two time points doesn't overlap (so does the pial and white surfaces from two points they appear on two distinct places on the freeview instead of being overlaped as shown in tutorial) when I load then it looks like there is some registration problem. I don't know where I made a mistake and how to correct for this. Any help will be greatly appreciated. Thanks Venkat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Statistics on longitudinal data
by Rajagopalan, Venkateswaran 02 Aug '12

02 Aug '12

Hi All, I am trying to do cortical thickness analysis on a single subject's longitudinal data. I am attaching the design and group.diff.mtx could any one tell me whether they are correct. Any web link (tutorial) on how to do stats on longitudinal data available. Thanks venkat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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(no subject)
by Hugh Pemberton 01 Aug '12

01 Aug '12

Hi, So when using command tkmedit *subjID* brainmask.mgz -aux -wm.mgz -surfs I receive the message: "Error: Parsing -aux option Expected an argument This option needs an argument: the image type, directory, or file name of the data to load as the aux volume." My apologies if there is an obvious answer but I can't see what is wrong (there are wm.mgz files in all subject directories), plus there doesn't seem to be anything missing as a result of this error message. Cheers for your help, Best, Hugh

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Freesurfer August 2012