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 ___ 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] Troubleshooting - uncertainty about adding control points
Hi Bruce, thanks for your answer! Am 30.01.2014 um 14:40 schrieb Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Janosch it's impossible to tell from a single slice whether those points should be added or not. The white matter in your image is *very* dark in these regions, do you know why? No, I don't know why, is that something to worry about? The screen shot is from a child participant, but it seems my images (includung the ones from adults) are darker than the ones provided in the tutorial overall. We used an optimized MDEFT sequence with the following settings Slices 176 Voxel size 1x1x1mm Orientation sagittal FoV 256x224 Matrix 224x256 TR 7.92 FA 16 TE 2.48 TI 910 PAT modeGrappa 2 Fat suppr fat sat Coil8ch. Head Bandwidth 195 Phase enc.dir A-P see Deichmann, R., Schwarzbauer, C., Turner, R. (2004). Optimisation of the 3D MDEFT sequence for anatomical brain imaging: technical implications at 1.5 and 3 T. NeuroImage, 21(2), 757–767. To decide whether to add them or not you should check a couple of slices in each direction (or look in multiple orientations) to make sure that the white matter is actually dark and it's not partial volume effects. The approach I would take is iterative - add a couple then rerun up to the first inflation and see if things have been improved significantly. This is fast, maybe 5-10 minutes, not sure. Thanks, I will try this approach. You shouldn't need to add a ton. Even one control point in the middle of a dark region can have a large effect. I still wonder which is the desired outcome state. Is it important that the white matter border follows *exactly* the one I perceive on every slice or is it OK when on some sclices it does not. Regarding the tutorial data: Can cp_after considered to be a completely corrected example subject or is only the one area corrected that the tutorial points to and the rest of the images would also have to be modified?! I see some areas in cp_before AND cp_after where I am not sure whether adding control points would be needed. It would help me if you could point me to one or two completely corrected and perfectly processed images so I could determine what level of accuracy is desirable. Sorry for all these questions, but I think modifying the images is a crucial point in the process that influences all further steps, and I just don't yet have a feeling for it... Thanks, Janosch cheers Bruce On Thu, 30 Jan 2014, Janosch Linkersdörfer wrote: 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 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] longitudinal processing, template and flags
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 dani...@ull.es Date:01/31/2014 3:41 AM (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edu,mreu...@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___ 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] 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 mreu...@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_freeview 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 listfreesur...@nmr.mgh.harvard.eduhttps://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: mreu...@nmr.mgh.harvard.edu reu...@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. ___ 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] Troubleshooting - uncertainty about adding control points
Hi Janosch there should be some corrected subjects in the tutorial. The white matter surface shouldn follow the perceived boundary, although it may look wrong when it is when it is curving sharply out of plane. I don't have much experience with MDEFT, so I can't comment on the parameters cheers Bruce On Fri, 31 Jan 2014, Janosch Linkersdörfer wrote: Hi Bruce, thanks for your answer! Am 30.01.2014 um 14:40 schrieb Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Janosch it's impossible to tell from a single slice whether those points should be added or not. The white matter in your image is *very* dark in these regions, do you know why? No, I don't know why, is that something to worry about? The screen shot is from a child participant, but it seems my images (includung the ones from adults) are darker than the ones provided in the tutorial overall. We used an optimized MDEFT sequence with the following settings Slices 176 Voxel size 1x1x1mm Orientation sagittal FoV 256x224 Matrix 224x256 TR 7.92 FA 16 TE 2.48 TI 910 PAT modeGrappa 2 Fat suppr fat sat Coil8ch. Head Bandwidth 195 Phase enc.dir A-P see Deichmann, R., Schwarzbauer, C., Turner, R. (2004). Optimisation of the 3D MDEFT sequence for anatomical brain imaging: technical implications at 1.5 and 3 T. NeuroImage, 21(2), 757–767. To decide whether to add them or not you should check a couple of slices in each direction (or look in multiple orientations) to make sure that the white matter is actually dark and it's not partial volume effects. The approach I would take is iterative - add a couple then rerun up to the first inflation and see if things have been improved significantly. This is fast, maybe 5-10 minutes, not sure. Thanks, I will try this approach. You shouldn't need to add a ton. Even one control point in the middle of a dark region can have a large effect. I still wonder which is the desired outcome state. Is it important that the white matter border follows *exactly* the one I perceive on every slice or is it OK when on some sclices it does not. Regarding the tutorial data: Can cp_after considered to be a completely corrected example subject or is only the one area corrected that the tutorial points to and the rest of the images would also have to be modified?! I see some areas in cp_before AND cp_after where I am not sure whether adding control points would be needed. It would help me if you could point me to one or two completely corrected and perfectly processed images so I could determine what level of accuracy is desirable. Sorry for all these questions, but I think modifying the images is a crucial point in the process that influences all further steps, and I just don't yet have a feeling for it... Thanks, Janosch cheers Bruce On Thu, 30 Jan 2014, Janosch Linkersdörfer wrote: 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 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 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
Re: [Freesurfer] Longitudinal analysis within one group
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.manzo...@gmail.com Date:01/31/2014 7:27 AM (GMT-05:00) To: Martin Reuter mreu...@nmr.mgh.harvard.edu Cc: Douglas Greve gr...@nmr.mgh.harvard.edu,free surfer freesurfer@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 mreu...@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_freeview 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@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: mreu...@nmr.mgh.harvard.edu reu...@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. ___ 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] brainmask VS wm correction
Hi Elisa it's tough to tell from just the wm.mgz image. Are the voxels excluded from the pial brain or are they dura? What does the orig surface show? If the orig doesn't follow the wm.mgz and you think it should, that means there is a topological defect that was inaccurately corrected and you need to fix that cheers Bruce On Fri, 31 Jan 2014, elisa veronese wrote: 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, Italy ICBN Website: http://icbn.uniud.it/tiki-index.php ___ 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] bbregister and AFNI
On 01/30/2014 06:34 PM, Ajay Kurani wrote:
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.
Neither bbregister nor tkregister2 apply the transform
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)?
You have to use --fstarg in this case because that was the target when
you ran bbregister
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?
Yes, in the header.
I'm not sure what you are trying to do here. Usually, one runs
bbregister using the middle time point as the mov template and one runs
motion correction separately to the middle time point. One then applies
the bbregister transform to the motion corrected time series to map it
to the surface (mri_vol2surf) or another volume (mri_vol2vol).
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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--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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] mri_convert - Scaling of Values
Hi Dan I think specifying -ns 1 will do the trick cheers Bruce On Fri, 31 Jan 2014, Daniel Carey wrote: 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.ca...@bbk.ac.uk web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey ___ 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] mri_convert - Scaling of Values
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.ca...@bbk.ac.uk web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey___ 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] mri_convert - Scaling of Values
what is your mri_convert command line. Send the terminal output too. doug On 01/31/2014 12:14 PM, Daniel Carey wrote: 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.ca...@bbk.ac.uk mailto:d.ca...@bbk.ac.uk web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] adding color scale to freeview
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 ___ 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] LGI ERROR: make_roi_paths did not complete successfully!
Hi Marie, Yes, I'm using matlab R3013a. In $FREESURFER_HOME/matlab folder I don't have a file called SearchProjectionOnPial.m. Should I create it and paste the updated function? Thanks for your help!! Wanda On 30 January 2014 15:09, Marie Schaer marie.sch...@unige.ch wrote: Hi Wanda, I'm not sure to understand your problem. Do you get an error because of using matlab 2013? If yes, I'm not sure to understand whether you modified the SearchProjectionOnPial.m function properly. Can you download the updated function there: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html and copy it in the $FREESURFER_HOME/matlab folder (replace the older one with this one). Let me know how it works, Marie On Jan 30, 2014, at 1:50 PM, Wanda Truong wanda.truong...@gmail.com wrote: Hello Marie, I am trying to conduct a local gyrification index analysis, however I am getting this error ERROR: make_roi_paths did not complete successfully! Which is the same as the one posted earlier by someone else: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032203.html I added the patch: function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, step) % step is typically set between 5 and 10. Default is 7, increasing it will % limit redundancies in the resulting path file. verticeslist=[]; si=max(size(perim)); for t=1:step:si [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); verticeslist= [verticeslist nearestIndexMT]; end verticeslist=unique(verticeslist); to my $freesurfer_home/matlab directly as a .m file. However, I'm still getting the same error: Error in dsearchn (line 80) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); ERROR: make_roi_paths did not complete successfully! Darwin Vinas-iMac.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 recon-all -s SFS026 exited with ERRORS at Thu Jan 30 14:26:16 MST 2014 Thanks, Wanda -- Wanda Truong, MSc ___ 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. -- Wanda Truong, MSc ___ 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] Recon-all error
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: e...@nmr.mgh.harvard.edu recon-all.log Description: Binary data recon.bash Description: Binary data ___ 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] Recon-all error
Emad, please run mri_converrt /Users/louispuybasset/Desktop/Zebouni_Fadi/T1/IM-0002-0001.dcm junk.mgh and send us the terminal output On 01/31/2014 03:28 PM, Emad Ahmadi wrote: 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: e...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] ERROR: dimension mismatch between y and X.
that looks like the right size. I am stumped. What version of FS are you using? Do you have access to other versions? On 01/31/2014 02:50 PM, Wanda Truong wrote: This is what I get: [Vinas-iMac:Wanda_SFS/qdec/Untitled] vinagoghari% ls -l y.mgh -rw-r--r-- 1 vinagoghari staff 1055844047 30 Jan 14:54 y.mgh On 31 January 2014 12:41, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: OK, it is y.mgh that is definitely wrong. Can you send me the result of ls -l y.mgh On 01/31/2014 02:37 PM, Wanda Truong wrote: Hi Doug, Here's what I get for mri_info lh.area.fwhm10.fsaverage.mgh: [Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_info lh.area.fwhm10.fsaverage.mgh Volume information for lh.area.fwhm10.fsaverage.mgh type: MGH dimensions: 163842 x 1 x 1 x 46 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 46 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0. : x_a = 0., y_a = 0., z_a = 1., c_a = 0. : x_s = 0., y_s = -1., z_s = 0., c_s = 0. talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 81921. 0. 0. 1.-0.5000 0. -1. 0. 0.5000 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 81921. -0. -0. -1. 0.5000 -0. 1. -0. 0.5000 0. 0. 0. 1. [Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_info /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh Volume information for /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh type: MGH dimensions: 163842 x 1 x 1 x 1584 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1584 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0. : x_a = 0., y_a = 0., z_a = 1., c_a = 0. : x_s = 0., y_s = -1., z_s = 0., c_s = 0. talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 81921. 0. 0. 1.-0.5000 0. -1. 0. 0.5000 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 81921. -0. -0. -1. 0.5000 -0. 1. -0. 0.5000 0. 0. 0. 1. Thank you! Wanda On 30 January 2014 15:30, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I don't know, it is a bit bizarre. Can you run mri_info on both lh.area.fwhm10.fsaverage.mgh and Untitled/y.mgh and send me the results? On 01/30/2014 05:01 PM, Wanda Truong wrote: Hi Doug, Same thing happens with the other half. I'm wondering what file is used for Y - is it lh.area.fwhm10.fsaverage.mgh? and why does it have an input number that is different from X, which should be the number of subjects?
Re: [Freesurfer] LGI ERROR: make_roi_paths did not complete successfully!
Hi Wanda, You should have this function in $FREESURFER_HOME/matlab, the same way you should have compute_lgi.m and many other matlab functions there. Are you sure that you are looking at the correct location and / or that you didn't delete it? Marie On Jan 31, 2014, at 11:32 AM, Wanda Truong wanda.truong...@gmail.commailto:wanda.truong...@gmail.com wrote: Hi Marie, Yes, I'm using matlab R3013a. In $FREESURFER_HOME/matlab folder I don't have a file called SearchProjectionOnPial.m. Should I create it and paste the updated function? Thanks for your help!! Wanda On 30 January 2014 15:09, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Wanda, I'm not sure to understand your problem. Do you get an error because of using matlab 2013? If yes, I'm not sure to understand whether you modified the SearchProjectionOnPial.m function properly. Can you download the updated function there: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html and copy it in the $FREESURFER_HOME/matlab folder (replace the older one with this one). Let me know how it works, Marie On Jan 30, 2014, at 1:50 PM, Wanda Truong wanda.truong...@gmail.commailto:wanda.truong...@gmail.com wrote: Hello Marie, I am trying to conduct a local gyrification index analysis, however I am getting this error ERROR: make_roi_paths did not complete successfully! Which is the same as the one posted earlier by someone else: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032203.html I added the patch: function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, step) % step is typically set between 5 and 10. Default is 7, increasing it will % limit redundancies in the resulting path file. verticeslist=[]; si=max(size(perim)); for t=1:step:si [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); verticeslist= [verticeslist nearestIndexMT]; end verticeslist=unique(verticeslist); to my $freesurfer_home/matlab directly as a .m file. However, I'm still getting the same error: Error in dsearchn (line 80) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); ERROR: make_roi_paths did not complete successfully! Darwin Vinas-iMac.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 recon-all -s SFS026 exited with ERRORS at Thu Jan 30 14:26:16 MST 2014 Thanks, Wanda -- Wanda Truong, MSc ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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. -- Wanda Truong, MSc ___ 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.
