Freesurfer

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30097 discussions

Re: [Freesurfer] jittered ITI and null trials fao Doug Greve
by Lukito, Steve 16 Aug '13

16 Aug '13

Hi Doug, Thanks for your response. I've been trying to build the sequence with your advice but I am still stuck. For the study we want to replicate, we will use TR=2s and we have 3x stimulus type (N=20) presented for 1s each. We gave a window of 1s for participant to respond. On top of this, we add jittered ITI (M= 1000ms; Range 750-1250ms, randomized psychological jitter to prevent participant to anticipate the trial). To deconvolve the MRI signal we want to have null blocks (length=2s per block) that are scattered in the sequence. I used the tnullmin tnullmax to build in the psychological ITI but then realize this was not a good idea b/c tnullmin and max has to be integer multiple of the dPSD. So the only way I thought of achieving the above is to remove the psychological jitter, and include the response time window into tEv and write the below line. I thought I will add the randomized psychological jitter after the sequence is built. optseq2 --ntp 80 --tr 2 --psdwin 0 12 2 --ev ConA 1 20 --ev ConB 1 20 --ev ConC 1 20 --evc 1 -1 0 --focb nCB1Opt --nkeep 3 --nsearch 100000 --o MRIsequence While the sequence is written fine, I suppose I no longer have an optimum sequence b/c my tEv is not correctly defined. Also the additional psychological jitter will change the assumption upon which the optimum sequence is built. Would really appreciate your thoughts on this. Best, Steve

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cortex stats
by _andreia_＠sapo.pt 16 Aug '13

16 Aug '13

Dear list, To obtain the thickness, surface area and volume values for each hemisphere I ran the command line in the subjdir: mris_anatomical_stats -mgz -f ../stats/lh.cortex_white.stats subjid lh white And did that with the pial surface too. However, the values I get from the generated cortex.stats do not match the ones in aparc.stats How can I get the referred measures, which are in the aparc.stats but do not appear in the table when using aparcstats2table? Thank you! Andreia

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cortical thickness visualization tools
by Muhammad Naveed Iqbal Qureshi 16 Aug '13

16 Aug '13

Dear list members, I want to make figures of the freesurfer analyzed data. So far I am using only surfstat toolbox for this purpose. Does anyone know any other tool for better visualization of thickness files. besides this how can I process the thickness files statistically - Can any software tool read this thickness as numeric value? Thank you. Best Regards, Muhammad Naveed Iqbal Qureshi P please don't print this e-mail unless you really need to

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Re: [Freesurfer] Finding a reference..
by jh kim 16 Aug '13

16 Aug '13

Thanks Alex. It would be of great help to me. Kim 2013/8/16 Alex Hanganu <al.hanganu(a)yahoo.ca> > Hi, > > I remember only finding articles that talked about the limitations of VBM. > Attached are some examples. > > Alex. > > > > > Le 15/8 9:37, jh kim a écrit : > > Dear experts > > Just a simple question. > Is there a published study that showed a superiority of cortical thickness > analysis (i.e., FreeSurfer) over VBM approach in assessing cortical grey > matter changes in brain disorders? > If so, please let me know. > > Thanks in advance for your help. > > Kim > > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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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Fwd: --sum option in mri_segstats
by charles laidi 15 Aug '13

15 Aug '13

Dear Freesurfers, I have a problem using the "mri_segstats" function. I'm trying to get Intra cranial volumes (ICV) from images that I have previously segmented. As I have lots of images, I'm using this script : " foreach filename (*_conv) mri_segstats --subject $(filename) --etiv-only --sum summaryfile end " The script is working very well except for the -sum option : I'm not able to find the summary file in my directory : the ICV are printed in my Terminal but I don't get all the ICV in a summary file. My ultimate goal is to import the ICV in an excel sheet... My question is : where can I find the summary file ? Should I specify after the -sum option an existing text file ? I don't understand how the -sum option works. Is there a function, like in "asegstats2table", that allows to directly get all the output of mri_segstats in a table ? I wasn't able to find an answer to my question in freesurfer wiki or in the mailing list messages. Thanks a lot for your attention, Best regards, Charles

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Re: [Freesurfer] Trac Stats
by Anastasia Yendiki 15 Aug '13

15 Aug '13

I didn't suggest taking it off, I meant make sure that the '/' is there, because the error message suggested to me that a '/' was missing from a filename listed IN that text file. Check your original error message. On Thu, 15 Aug 2013, Alan Francis wrote: > Hi Anastasia: > > I took off the '/' before the autofs, but then it gave me a different > problem. > > csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ > recons] : tractstats2table --load-pathstats-from-fileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_re > cons/Forceps_Major_CC.list.txt --overall --tablefileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_re > cons/Forceps_Major_CC.All.table > > ERROR: the fileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_re > cons/Forceps_Major_CC.list.txt doesnt exist > > Actually it does exist. > > thanks, > > Alan > > > On Thu, Aug 15, 2013 at 2:40 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Is it really autofs without the '/' in front? > > On Thu, 15 Aug 2013, Alan Francis wrote: > > Hi Anastasia: > > Sorry to bother you again. I am trying to extract trac > stats from the FS > data. When I run the following script, it gives me an > error message: > > csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5 > .3_Data/diffusion_ > recons] : tractstats2table--load-pathstats-from-file/autofs/space/dali_003/users/BW_project_DTI/FreeS > urfer_5.3_Data/diffusion_r > econs/Forceps_Major_CC.list.txt --overall--tablefile/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/ > diffusion_r > econs/Forceps_Major_CC.All.table > > Parsing the .stats files > > ERROR: The statsfileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusio > n_re > cons/BW_101/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt > is not found > or is too small to be a valid statsfile > > However, when I manually checked the pathstats.overall.txt, the > data is > physically there. Am I doing something wrong? > > thanks so much, > > Alan > > > > > 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. > > > >

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create label from cluster obtained with mri_glm-fit-sim
by Garikoitz Lerma-Usabiaga 15 Aug '13

15 Aug '13

Hi list, we have a cluster that survived the Monte Carlo simulation for thickness, and we would like to obtain more data from that exact cluster (volume for example), is it possible to automatically create a label from that cluster? If I use mri_binarize or mri_cor2label is not working (I understand that the clusters are not stored as individual vertexes in the .mgh file but I don't know what the format is. Thanks in advance! Gari PD: I am on a VPN and tksurfer is not working for manually creating a label with the contour of the cluster.

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Trac Stats
by Alan Francis 15 Aug '13

15 Aug '13

Hi Anastasia: Sorry to bother you again. I am trying to extract trac stats from the FS data. When I run the following script, it gives me an error message: csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : tractstats2table --load-pathstats-from-file /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/Forceps_Major_CC.list.txt --overall --tablefile /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/Forceps_Major_CC.All.table Parsing the .stats files ERROR: The stats file autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_101/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt is not found or is too small to be a valid statsfile However, when I manually checked the* pathstats.overall.txt, *the data is physically there. Am I doing something wrong? thanks so much, Alan

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Bus error for tkmedit and tksurfer
by ye tian 15 Aug '13

15 Aug '13

Dear Freesurfers, Tkmedit and tksurfer both return "Bus error" for me. I can even have a glimpse of the surfaces before tksurfer collapses on me. I checked the archive http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19422.html I don't think disc space is an issue for me since the freesurfer is installed and run on a portable hard drive with >600GB of free space. Thank you very much for your help in advance! Sincerely, Ye

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Antw: Re: [tracula] error running trac-all -prep
by Borsodi Florian 15 Aug '13

15 Aug '13

Hi Anastasia I ran the command you sent me and it runs without any errors. I also attached the command line for you. Furthermore i ran data with 12 diffusion directions and i keep getting the same kind of problems. sincerely Florian >>> Anastasia Yendiki 02.08.13 19.59 Uhr >>> Hi Florian - Can you please run this command directly on the command line and see if there are any errors? flip4fsl /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz Thanks, a.y On Fri, 2 Aug 2013, Borsodi Florian wrote: > Hi Anastasia > > Thank you for your answer. > > Yes, those files exist. > I also extracted the bvec an bval files with anotther software then dcm2nii > and i keep getting the same kind of error. > Also, about the 6 diffusion direction, those data i sent you, are just > testdata for running tracula. > > sincerely > Florian > > >>> Anastasia Yendiki 02.08.13 0.41 Uhr >>> > > Hi Florian - Do these files exist? > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvecs > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvals > > > The format of the bvecs and bvals that you sent seems fine, but (and this > has nothing to do with the error you're getting) I have to warn you that > you may not be able to get good results running probabilistic tractography > on this data. It looks like you're acquiring the same 6 diffusion > directions, repeated 8 times. Six directions is the absolute minimum for > reconstructing the tensor model, but will probably not be sufficient for > the crossing fiber model that bedpostx reconstructs (and is used by > tracula). Your scan time is better spent acquiring 48 different > directions, rather than the same 6 directions 8 times. > > a.y > > On Mon, 29 Jul 2013, Borsodi Florian wrote: > > > Hello, > > > > I have been trying to run tracula on my data and i keep getting the same > > kind of error repeatedly. > > For my imput I am using dicoms from a Siemens scanner with a stadard > > diffusion protocol. However, tracula cannot read the bvec and bval data > out > > of the dicom header. Therefore, I implemented bvec and bval files into the > > config file. > > After doing so, I got the error which says that tracula cannot find the > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > > I have tried many options, but still cannot find a solution. > > I am hoping to get some troubleshooting help. > > > > I have atteched my log- and config- files, as well as my bvec and bval > > files. > > To uphold patient confidentiality, I have encode the name patient's data > as > > "AAAAAA". > > > > I believe the problems are the bvec and bval files or their structures. > The > > log-file lete me assume this, especially the lines 202 - 205, 264 - 268 > and > > 1480 - 1484. > > > > Thank you in advance for your help, and your speedy response. > > > > With kind regards, > > > > Florian Borsodi > > Department of Neurology > > Medical University of Graz > > > > > > > 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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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