Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

130 participants
211 discussions

Recon-all error
by Emad Ahmadi 31 Jan '14

31 Jan '14

Hello, I am using recon-all, and it gives me error and exits and I cannot understand why. I would appreciate it if you give me a clue why it's not working. I've written a piece of script (recon.bash attached) to be copied to the subject's folder, and when run it should automatically go through the analysis pipeline, but it gives me the error and exits. Thank you very much, Emad Emad Ahmadi, MD ------------------------------------------------ Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

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adding color scale to freeview
by Fred Lado 31 Jan '14

31 Jan '14

Dear Freesurfer Experts, Is there a way to create custom color scale - like “Heat”, “Jet”, etc - for use in Freeview? Thanks, Fred Lado Montefiore Medical Center

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mri_convert - Scaling of Values
by Daniel Carey 31 Jan '14

31 Jan '14

Dear All, We have been using mri_convert to convert .nii format quantitative scans (specifically R1 volumes) into .mgz (float) format, so they can be used as input to mri_vol2surf. Inputting the .nii files to mri_vol2surf has produced an error in values in the output paint file, whereas this issue appears not to occur with the .mgz input. In running mri_convert, we are encountering an issue with the scaling of image values. Optimally, we would like to preserve the values within the quantitative volume, such that mri_convert does not change these when we output to .mgz. In some cases, we have noted non-linear differences in the output .mgz values, compared to the input volume. We have been using the -ns flag, and still see these issues. Is there a way to set the output .mgz scale factor to preserve the existing values exactly as per the quantitative input volume? Any advice would be greatly appreciated. Many thanks in advance. Best wishes, Dan --- Daniel Carey Marie Curie Ph.D. Fellow, Centre for Brain and Cognitive Development, 32 Torrington Sq., London WC1E 7HX UK email: d.carey(a)bbk.ac.uk web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey

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bbregister and AFNI
by Ajay Kurani 31 Jan '14

31 Jan '14

Hi all, I used freesurfer to process my anatomical scans, followed by BBregister to align my resting state scan to the anatomical and finally afni to process the resting state fmri scans. After recon-all I used bbregister: *bbregister -s ${sub}_FS --mov ${sub}.RS.nii --reg $sub_RS_register.dat --init-header --bold --frame $LAST --nearest --template-out $sub.RS.template.nii* I used the following for manual adjustments (although none were needed!) *tkregister2 --mov $sub.RS.template.nii --reg $sub_RS_register.dat --surf* The plan is to apply the reg file to the entire resting state timeseries ($sub.RS.nii). My question is the following: 1) Does bbregister already move the last timepoint in $sub.RS.nii as well as $sub.RS.template.nii or does it just store the rigid transformation in the reg file (this is what I assume)? This is the reason I assume we supply reg into tkregister2 as I assume the transform is not applied to the nifti file header itself. 2) Assuming the transformations are not applied to the file itself, how would I go about doing this? I used the following based on previous posts: *mri_vol2vol --mov $sub.RS.nii --reg $sub_RS_register.dat --fstarg --interp nearest --o $sub.RS.align.nii --precision short --no-resample * I used no-resample as I do not want to put the data into orig space. The plan is to align all of my timepoints to the last time point (same as $sub.RS.template.nii). ----Is --fstarg the best option (default orig.mgz vs --fstarg rawavg.mgz)? ----Is the transform stored in the header of $sub.RS.align.nii and not in the $sub.RS.template.nii file or $sub.RS.nii? 3) Using @SUMA_Make_Spec_FS did not correctly convert brain.mgz and aseg.mgz correctly when overlaid with the original $sub.SPGR.FS.mgz as well as $sub.RS.align.nii or $sub.RS.nii so I just used the following instead /mri directory: *mri_convert -ot nii brain.mgz brain.nii* *mri_convert -ot nii aseg.mgz aseg.nii* *4) Following relates to viewing images created in AFNI correctly if anyone knows: * When I tried to use AFNI to view the original anatomical scan $sub.SPGR.FS.mgz and $sub.RS.align.nii it was not aligned (assume anatomical is similar to rawavg.mgz). When I load brain.nii and $sub.RS.align.nii into afni they are not overlapped perfectly as in tkregister2. Additionally I get an error about deobliquing the $sub.RS.align.nii file. Interestingly enough I do not get this error with the $sub.RS.template.nii so I am not sure if there is an error in applying the transform or if the template file has no transform info stored while the aligned file does. How would I apply the reg file to all timepoints without getting the oblique error or should I use the following command and is this correct: *3dWarp -deoblique -gridset $sub.RS.nii -prefix $sub.RS.align.deobl.nii $sub.RS.align.nii* Would i deoblique using the gridset of the original $sub.RS.nii, the aligned file $sub.RS.align.nii or just the template file (or does it not matter since the voxel dimensions are the same even though centers are different). Sorry for the long email but thanks in advance for any advice / explanations. Sincerely, Ajay

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brainmask VS wm correction
by elisa veronese 31 Jan '14

31 Jan '14

Dear all, I am trying to manually correct the segmentation result in one subject. My problem is that I am not sure if in the area highlighted with the green circle (see attached file) the volume I should correct is the brainmask.mgz or the wm.mgz. The pial boundary looks uncorrect, so I'd correct the brainmask. But those voxels seem to belong to the wm.mgz volume, as well... Thank you. Best, Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php <http://icbn.uniud.it/tiki-index.php>*

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Re: [Freesurfer] Longitudinal analysis within one group
by Martin Reuter 31 Jan '14

31 Jan '14

Given the different time distances, the best would be mixed effects models. The 2 stage model should also work as it incorporates time (but not different correlations according to time distance). Again I don't see what you are analyzing with only one group. There will always be thinning, and you will find it in some regions more than in others (depending on how much power you have). Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: amirhossein manzouri <a.h.manzouri(a)gmail.com> Date:01/31/2014 7:27 AM (GMT-05:00) To: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Cc: Douglas Greve <greve(a)nmr.mgh.harvard.edu>,free surfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal analysis within one group Dear Doug and Martin, Thanks a lot. I just have one group including 20 subjects. The scans have been done in a range of 0.9 to 1.5 years difference (tp2-tp1). Is ooh if I use the instructions from Paired Analysis :https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis ? Regards, Best regards, Amirhossein Manzouri On Thu, Jan 30, 2014 at 10:31 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi, with one group you want to check if atrophy is significantly different from zero? That is probably the case for any group (e.g. aging), so it won't tell you anything really. Also, if you don't find atrophy in a region it doesn't mean it's not there (only your group size is too small to detect it). So the only real use I can think of, would be a test-retest study, where the assumption is that there is no change? Sadly Qdec cannot do 'one sample group mean', otherwise you could do that in qdec. If only you had a second 'control' group, then it could be done. You can use long_mris_slopes to compute rate or percent change maps (one for each subjects) and then you can use qdec to analyze those rate maps across groups. If you don't have a control group, you could still use long_mris_slopes (it can also map and stack the rate maps on fsaverage) and then simply run the one sample group mean in mri_glmfit. some info is also here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial_f… and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel Best, Martin On 01/30/2014 09:18 AM, amirhossein manzouri wrote: Hi, Would you please advise if it is possible to do longitudinal statistical analysis within a group with two time points in Qdec. And if it is not possible in Qdec how I suppose to do it? Best regards, Amirhossein Manzouri _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu 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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Troubleshooting - uncertainty about adding control points
by Janosch Linkersdörfer 31 Jan '14

31 Jan '14

Dear Freesurfers, I am just getting started using Freesurfer. I ran recon-all on my subjects for the first time and now would like to troubleshoot the output. I watched the tutorial lectures and worked through the troubleshooting tutorial. Nevertheless, I am still uncertain which things I will have to correct (especially as editing too much and/or not to the same degree between subjects might do more harm than good). Some errors are relatively obvious like the exclusion of white matter voxels from the white matter surface (see *1* on the screen shot of my own data) I am far more uncertain about adding control points. For example, I do not know whether I should add those at the location denoted with *2* in my own data. If so, there would be a lot of other, similar locations where I would add control points in my data. But this would also be true for the image used in the "Adding control points" tutorial. In the second screen shot, which displays this image, I have marked some locations where the white matter surface does not follow the one I would draw if I had to do it manually. Is one supposed to correct all those imprecisions by adding control points?! What are the criteria for adding vs. not adding control points? Thank you very much, Janosch

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Re: [Freesurfer] longitudinal processing, template and flags
by Martin Reuter 31 Jan '14

31 Jan '14

Hi Daniel, I'd also include 24 month into both the processing and analysis. It is not really that we are trying to improve a registration here. We are trying to improve segmentation and surface placement of each time point. I'd aways use all data, except there are good reasons to drop (eg strong motion artifacts). Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Daniel Ferreira <danifer(a)ull.es> Date:01/31/2014 3:41 AM (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edu,mreuter@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal processing, template and flags Thanks Martin for your reply, I am agree with you on point 1. What would you say in the case that we are interested in rates of decline from baseline to 12 months, but besides 6 months follow-up we also have 24 months?. Here I see more conceptual problems. In an hypothetical context of severe atrophy from 12 to 24 months, adding the 24 mo follow-up perhaps difficult registration more than improves it. What do you think? Thanks a lot Best Daniel Hi Daniel, 1. yes. But why not include 6 month in your study if you have those scans??? You will get much more reliable slope estimates with 3 time points compared to 2, so including that time point will not only help for the image processing part, but also in your statistics (you gain power). 2. I am not familiar with the mprage flag and think it mainly affects the normalization. If you are sure you need it, then also add it to the -base and -long runs, just to be safe. best, Martin On 01/29/2014 09:08 AM, Daniel Ferreira wrote: Dear experts, I have two questions regarding the longitudinal stream: - I am including Baseline and 12 months follow-up in my study. However, I also have 6 months follow-up. I wonder if it is conceptually right to include these 6 months scans in template creation with the idea of increasing registration. - I am applying the -mprage flag in the crossectional first step. Should I use it in the -base and -longs steps too? Thanks very much Daniel Ferreira

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Longitudinal analysis within one group
by amirhossein manzouri 31 Jan '14

31 Jan '14

Hi, Would you please advise if it is possible to do longitudinal statistical analysis within a group with two time points in Qdec. And if it is not possible in Qdec how I suppose to do it? Best regards, Amirhossein Manzouri

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Re: [Freesurfer] longitudinal processing, template and flags
by Daniel Ferreira 31 Jan '14

31 Jan '14

Thanks Martin for your reply, I am agree with you on point 1. What would you say in the case that we are interested in rates of decline from baseline to 12 months, but besides 6 months follow-up we also have 24 months?. Here I see more conceptual problems. In an hypothetical context of severe atrophy from 12 to 24 months, adding the 24 mo follow-up perhaps difficult registration more than improves it. What do you think? Thanks a lot Best Daniel Hi Daniel, 1. yes. But why not include 6 month in your study if you have those scans??? You will get much more reliable slope estimates with 3 time points compared to 2, so including that time point will not only help for the image processing part, but also in your statistics (you gain power). 2. I am not familiar with the mprage flag and think it mainly affects the normalization. If you are sure you need it, then also add it to the -base and -long runs, just to be safe. best, Martin On 01/29/2014 09:08 AM, Daniel Ferreira wrote: Dear experts, I have two questions regarding the longitudinal stream: - I am including Baseline and 12 months follow-up in my study. However, I also have 6 months follow-up. I wonder if it is conceptually right to include these 6 months scans in template creation with the idea of increasing registration. - I am applying the -mprage flag in the crossectional first step. Should I use it in the -base and -longs steps too? Thanks very much Daniel Ferreira

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Freesurfer January 2014