Freesurfer November 2012

freesurfer@nmr.mgh.harvard.edu

105 participants
177 discussions

p-value too small?
by Caspar M. Schwiedrzik 26 Nov '12

26 Nov '12

Hi! I ran into a funny problem when calculating contrasts in Freesurfer 4.5.0. Namely, the center of my cluster of significant voxels has a p-value of -0.0, resulting in a funny whole where you would otherwise expect to find the most significant voxel(s). It seems that the p-value is too small. Is there a workaround available? Thank you very much, Caspar

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Re: [Freesurfer] Subgroup analysis
by Mahinda Yogarajah 26 Nov '12

26 Nov '12

Hi Doug and Donald, Again many thanks for the advice. With regard to the analysis described previously - I have n=21 in my control group while P1=4 patients, P2=7 patients, P3=3 patients and P4=5 patients. Given that i have small numbers I elected to compare only 2 patient groups (p1 and p4) rather than all 4. My aim was to show that P4 patients (higher level of endogenous factor) are more affected (eg smaller area and greater thickness-age decline compared to controls) than P1. Given that as Donald points out that (c-p1) - (c-p4) is like comparing p1 and p4 directly, I did the latter but there is nothing significant. However when i compare p1 to controls and then p4 to controls separately i see nothing signficant in the p1 analysis but significant results in the p4 analysis - this makes sense as the p4 gp are more affected than the very mild p1 gp. My questions are: 1) why the difference in results between the two analyses (? due to larger overall group in second analysis) 2) is the latter analysis valid ? Thanks for your help. Mahinda

2 1

topological defect correction: Orig surface is right but WM surface is not right
by 嘉逸劉 26 Nov '12

26 Nov '12

Hello FS experts, I have a MRI volume where there is regional hyperintensity at cortex and thus the segmentation takes that regional cortex as white matter. In other words, the segmentation process is too aggressive toward the pial surface. I modifed the WM by manual erase across several slices and run -autorecon2-wm and -autorecon3. However, when I checked the results, I found the "original surface" is right (green color in the appended file; the tesselation is compatible with my manural editing) but the "white matter surface" is not updated (yellor color in the appended file; the surface is not adjusted, just like the old one before my editing). Could anybody guide me how to solve this issue? Thank you very much, JoJo

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rotation applied by mri_convert
by Marie Schaer 26 Nov '12

26 Nov '12

Hi everyone, I have a question related to mri_convert (I use FreeSurfer version 5.1). I noticed that when I convert some images without specifying anything about the orientation (mri_convert MY_DICOMS 001.mgz), in a high proportion of the case, mri_convert will identify an orientation matrix which is not simply made of 0 and 1, like e.g. i_ras = (-0.00872651, -0.999962, 0) j_ras = (-0, -0, -1) k_ras = (-0.999962, 0.00872654, 0) The non integer values result in the application of a slight rotation when converting the images, associated with interpolation and a slight loss in image quality. The only way that I found to avoid that the image quality loss was to run a first time mri_convert to look at these parameters, and then transform them to the nearest integer to feed them to mri_convert. In the example above I would run: mri_convert MY_DICOMS 001.mgz -iid 0 -1 0 -ijd 0 0 -1 -ikd -1 0 0 Given that I don't change the orientation (i.e no flip), but just want to avoid the rotation, I was wondering if there was any better option in mri_convert than what I am currently doing. Many thanks in advance for your answer, Marie

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Info FreeSurfer
by Andrea Tateo 26 Nov '12

26 Nov '12

Hello, I am working on segmentation of the hippocampus and I need a comparing method. I am approaching for the first time to FreeSurfer method. I would like your courteous help. I have three questions for you: 1 - I have input a MRI-image.nii showing all head. As output I would like a binary image showing only left and right hippocampus. I used the following command: ### mri_convert FILE_NAME.nii path/directory/NAME_OUTPUT.mgz recon-all -s SUBJECT_name -autorecon-all ### How can I extract the required binary image? 2 - Is it possible to comput only hippocampus region (to reduce the processing time)? 3 - Is it possible to give as input only an ristrected region of the subject's head? Best regards Andre Tateo

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re reconstructions
by Catherine Bois 26 Nov '12

26 Nov '12

Hi, I am currently in the process of reconstructing my brains after performing edits. I am submitting them to a system named condor, which allows them to be processed in parallel, reducing time. However, I am unsure of how to best use the script that takes into account all the changes made. Is it possible to submit the same script for all (even though different changes have been made to each brain), as long as the command specifying the change occurs earlier in the process than for example the changes made to a certain brain (hope that makes sense). Is this correct? However, I have also heard from someone tha tif you make white matter edits you should only run the reconstruction process at the steps AFTER the white matter mask is created; is this correct? As this is contradictory to what I thought; I thought that you start with your edits that are "earlist in the process"; ie do that step again and then it takes into account subsequent edits? Thanks for your help, sorry for the confusing question. Cathy

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Re: [Freesurfer] R: RE: Info FreeSurfer
by Azeez Adebimpe 26 Nov '12

26 Nov '12

17 is the intensity value for left hippocamus, and 53 for the right hippocamus. Then you can view with tkmedit ( to view aseg.mgz) for more clearance. Then use matlab to extract this label base on the intensities value. Azeez Adebimpe Date: Mon, 26 Nov 2012 13:48:09 +0100 From: andrea.tateo(a)virgilio.it To: ayobimpe2004(a)hotmail.com Subject: R: RE: [Freesurfer] Info FreeSurfer Hi Azeez Adebimpe, thanks for your quick answer. I open the text file that you recommended me. What means these three numbers in the following string: 17 Left_Hippocampus 1.20 0.0 80 ? How can I use these information in MatLab? Andrea Tateo ----Messaggio originale---- Da: ayobimpe2004(a)hotmail.com Data: 26-nov-2012 13.19 A: <andrea.tateo(a)virgilio.it> Ogg: RE: [Freesurfer] Info FreeSurfer Hi AndreaYou cant restrict ouput of the freesurfer to only hippocamus but after the segmentation you can select the hippocamus both right and left base on intensity value ( check this doc inside mri subfolder: aseg.auto_noCCseg.label_intensities.txt). You can use matlab or any program to extract the hippocamus. Azeez Adebimpe Date: Mon, 26 Nov 2012 13:06:48 +0100 From: andrea.tateo(a)virgilio.it To: Freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Info FreeSurfer Hello, I am working on segmentation of the hippocampus and I need a comparing method. I am approaching for the first time to FreeSurfer method. I would like your courteous help. I have three questions for you: 1 - I have input a MRI-image.nii showing all head. As output I would like a binary image showing only left and right hippocampus. I used the following command: ### mri_convert FILE_NAME.nii path/directory/NAME_OUTPUT.mgz recon-all -s SUBJECT_name -autorecon-all ### How can I extract the required binary image? 2 - Is it possible to comput only hippocampus region (to reduce the processing time)? 3 - Is it possible to give as input only an ristrected region of the subject's head? Best regards Andre Tateo _______________________________________________ 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.

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Missing tracts in final TRACULA results
by Arman Eshaghi 26 Nov '12

26 Nov '12

Dear all, Following successful runs of 3 stages of trac-all script on an MS brain, I get the following result. As you might see right inferior longitudinal fasciculus (parital) and right uncinate fasciculus are missing. I was wondering at which stage the problem is most likely (prep, bedpostx, or the last step)? (recon-all results seem to be alright.) All the best, -Arman [image: Inline image 1]

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aseg.mgz not automatically upated after topological correction
by 嘉逸劉 24 Nov '12

24 Nov '12

Hi FreeSurfer experts, I have a question regarding how to update aseg.mgz after topological correction. I hope to use the labels in aseg.nii as the definition of ROIs (including the definition of white matter). After topological correction, the surfaces of white matter and pia are fine; the filled.mgz looks good. However, when I go back to check aseg.mgz, I notice that the boundary of white matter of aseg.mgz is not updated. Any suggestion is appreciated. Thanks, JoJo

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Please help: nu_correct crash problem
by Negar Memarian 24 Nov '12

24 Nov '12

Dear all, I'm very new to FreeSurfer and really appreciate your help: I installed FreeSurfer very recently and it's the first time that I need to run recon-all but unfortunately it crashes at the nu_estimate_np_and_em step with this error message: nu_estimate_np_and_em: crashed while running spline_smooth (termination status = 6) nu_correct: crashed while running nu_estimate_np_and_em (termination status = 65280) ERROR: nu_correct FYI, the recon-all.log file is attached. Also, not sure if it makes any difference or not, but I need to run recon-all for a subject whose images were imported from DICOM to mgz using recon-all -i Looking forward to your response. Thank you, Negar

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Freesurfer November 2012