Re: [Freesurfer] Segmentation of MR-PET structurals
Hi Gabriel, I don't have experience with the MR-PET yet. Why do you think there is a problem? Try running wm-anat-snr on this subject. In general, you don't want to be smoothing/denoising the anatomical doug On 6/18/13 1:13 PM, obre...@nmr.mgh.harvard.edu wrote: Hi, I've started segmenting several structural scans from an MR-PET study conducted in Bay 7, and was wondering if someone has previous experience working with MPRAGE images acquired using the MR-PET coils? The scans have a very low SNR and I am trying to figure out if this could potentially affect the performance of the automated surface reconstructions. I've scrolled through the volumes and even though the surfaces seem normal, I am somewhat skeptical about their true quality given that intermediate stages, such as the intensity normalization, seem to be failing (please find an example from one of the brain masks attached). Is it essential to filter the raw structurals before segmenting them, and if so, are there any readily available denoising tools? Furthermore, are there any additional issues I should take into consideration? Thanks for your help! Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] qdec differences in FS 5.0 vs 5.3
Hi Maria, can you elaborate on exactly what you have done? Is the data the same and you are only changing the version of QDEC? What is the nature of the difference? Can you send pics or stats? doug On 6/18/13 6:06 AM, Maria Kharitonova wrote: Hi, I'm learning how to use QDEC and was comparing results that it produces under FresSurfer 5.0 vs 5.3. I know the 5.0 has an option for either DODS or DOSS method of producing a design matrix, while the 5.3 only has DODS. This suggests that results should be identical (or at least similar) across versions if I select DODS. However, I'm getting very different results based on the version I select: complete lack of differences across groups in 5.3 and a predicted pattern of differences in 5.0 using DODS. I'd like to understand where the differences are stemming from -- any ideas? Thanks in advance! Maria *** Maria Kharitonova, Ph.D. Postdoctoral Research Fellow Laboratories of Cognitive Neuroscience Boston Children's Hospital ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] problem downloading Xhemi files
try now On 6/18/13 9:37 PM, amirhossein manzouri wrote: I have version 5.1 so please recreate the links! BR On Tue, Jun 18, 2013 at 8:43 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Amir, if you are using 5.2 or 5.3, then you should already have it. If not, I'll have to recreate the links. let me know doug On 6/17/13 6:52 AM, amirhossein manzouri wrote: Dear Doug, I can not download the files needed for Xhemi in mentioned link. Would you please advise how to download them? -- Best regards, Amir ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Best regards, Amirhossein Manzouri ___ 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] MRIread.m and hippocampal subfields
Hi Marcos, it is weird that the posterior*.mgz does not have that info.
Maybe Koen or Eugenio know why. In the mean time, you can use
mri_convert to change/set the parameters, eg
mri_convert in.mgz out.mgz -tr 0 -ti 0 -te 0 -flip_angle 0
doug
On 6/18/13 2:50 PM, Marcos Martins da Silva wrote:
Hi, Freesurfer experts
If you try to read one of the posterior*.mgz files generated by
reco-all -hippo-subfield into MatLab/Octave using MRIread.m it fails
like this:
*Ps=MRIread('posterior_left_subiculum.mgz') *
*WARNING: error reading MR params*
*Attempted to access mr_parms(1); index out of bounds because*
*numel(mr_parms)=0.*
*Error in MRIread (line 100)*
* tr = mr_parms(1);*
That is because the posterior*.mgz files does not have this data.I
made a creating a little customized nMRIread.m with the following
changes:
*if numel(mr_parms) 0*
* tr = mr_parms(1);*
*flip_angle = mr_parms(2);*
* te = mr_parms(3);*
* ti = mr_parms(4);*
* else*
*mr_parms(1) = 0;*
* mr_parms(2) = 0;*
* mr_parms(3) = 0;*
* mr_parms(4) = 0;*
* tr = mr_parms(1);*
* flip_angle = mr_parms(2);*
*te = mr_parms(3);*
*ti = mr_parms(4);*
* end*
That works but it is only a quick workaround since MRIread,m calls
load_mgh.m and it shows a warning message about the mr_parms. This
message does not block my work but it is not good to see the warning
all the time on my screen. Perhaps the best fix would be just creating
the posterior*.mgz files with these data defined as 0. But I would be
happy if I could just edit these files defining these values. Is
there a freesurfer tool to make this simple edition? I noticed, for
example, that when you use mri_concat to sum these files the resulting
concatenated file is fixed and these parameters are defined.
Thanks in advance,
Marcos.
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Re: [Freesurfer] problem downloading Xhemi files
I use curl to download in MAC with the links you mentioned and it is not there! amir% curl -O ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 0 00 00 0 0 0 --:--:-- 0:00:01 --:--:-- 0 curl: (78) RETR response: 550 On Wed, Jun 19, 2013 at 8:42 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: try now On 6/18/13 9:37 PM, amirhossein manzouri wrote: I have version 5.1 so please recreate the links! BR On Tue, Jun 18, 2013 at 8:43 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: Hi Amir, if you are using 5.2 or 5.3, then you should already have it. If not, I'll have to recreate the links. let me know doug On 6/17/13 6:52 AM, amirhossein manzouri wrote: Dear Doug, I can not download the files needed for Xhemi in mentioned link. Would you please advise how to download them? -- Best regards, Amir ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___ 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] TRACULA - tract volume and length
Dear DTI experts, I am trying to understand how to interpret tract length volume measurements that TRACULA provides. For example, let’s say a clinical population differs from a control group in mean FA of a particular tract, and tract length volume are comparable across the 2 groups. I think this would support the notion that the tract’s diffusion properties are indeed different across the two groups and that the FA finding are unlikely to be an artifact of probabilistic tractography. Is this a correct interpretation? Conversely, if group differences in tract volumes were detected, would you recommend comparing mean FA across the two group while covarying for tract volume? Thanks! ___ 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] Reviewer not satisfied
read_curv.m should do the trick On Wed, 19 Jun 2013, Jürgen Hänggi wrote: Dear Bruce Yes, the .max and the .min files were produced, but how to access the values in it. Is there a possibility to import these files into MATLAB? Thanks in advance Cheers Jürgen On [DATE], Bruce Fischl [ADDRESS] wrote: .H is mean and .K is Gaussian curvature. It should also write a .max and .min, doesn't it? Those are the principal curvatures that you want. Bruce On Tue, 18 Jun 2013, Jürgen Hänggi wrote: Dear Bruce Thanks a lot for the info. It worked fine, but how can I open the resulting .H and .K files? Cheers Jürgen On [DATE], Bruce Fischl [ADDRESS] wrote: Hi Jürgen you could quantify this if you want. Use mris_curvature to compute the mean curvature maps independently (the first and second principal curvatures). These have the units of 1/mm and are exactly the radius of curvature. You could histogram them and look at the distribution. cheers Bruce p.s. I think you want -w -max and -w -min flags for it On Fri, 14 Jun 2013, Jürgen Hänggi wrote: Dear FS experts In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition. We wrote the following: The thickness maps produced are not limited to the voxel resolution of the image and thus sensitive for sub-millimeter differences between groups (Fischl, Dale 2000). The way in which the resolution of the cortical thickness maps goes beyond the resolution of the original acquisition can be imagined as a (conventional) partial volume correction procedure. The cortex is smooth at the spatial scale of a couple of millimeters, which is imposed as constraint by FreeSurfer to estimate the location of the surface with subvoxel accuracy. For instance, if a given voxel is darker than its neighbouring grey matter it probably contains more CSF and so the surface model is at a slightly different position than if the neighbouring voxels were brighter and therefore contain probably more white matter. Now, the reviewer says that we are to vague in our description. He would like to know what is exactly meant by a couple of millimeters. Is this 1-3 mm or rather 3-5 mm or any other value? Thanks in advance for any suggestion Regards Jürgen Hänggi --- - Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. --- - ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ Freesurfer mailing list
Re: [Freesurfer] MRIread.m and hippocampal subfields
I knew you would have a clean solution. :-)
Thank you, Doug.
Em Ter, 2013-06-18 às 23:45 -0700, Douglas Greve escreveu:
Hi Marcos, it is weird that the posterior*.mgz does not have that
info. Maybe Koen or Eugenio know why. In the mean time, you can use
mri_convert to change/set the parameters, eg
mri_convert in.mgz out.mgz -tr 0 -ti 0 -te 0 -flip_angle 0
doug
On 6/18/13 2:50 PM, Marcos Martins da Silva wrote:
Hi, Freesurfer experts
If you try to read one of the posterior*.mgz files generated by
reco-all -hippo-subfield into MatLab/Octave using MRIread.m it fails
like this:
Ps=MRIread('posterior_left_subiculum.mgz')
WARNING: error reading MR params
Attempted to access mr_parms(1); index out of bounds because
numel(mr_parms)=0.
Error in MRIread (line 100)
tr = mr_parms(1);
That is because the posterior*.mgz files does not have this data. I
made a creating a little customized nMRIread.m with the following
changes:
if numel(mr_parms) 0
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
else
mr_parms(1) = 0;
mr_parms(2) = 0;
mr_parms(3) = 0;
mr_parms(4) = 0;
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
end
That works but it is only a quick workaround since MRIread,m calls
load_mgh.m and it shows a warning message about the mr_parms. This
message does not block my work but it is not good to see the warning
all the time on my screen. Perhaps the best fix would be just
creating the posterior*.mgz files with these data defined as 0. But
I would be happy if I could just edit these files defining these
values. Is there a freesurfer tool to make this simple edition? I
noticed, for example, that when you use mri_concat to sum these
files the resulting concatenated file is fixed and these parameters
are defined.
Thanks in advance,
Marcos.
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[Freesurfer] error in lme_mass_fit using matlab tools
Dear Freesurfer experts,
I have a question about fitting linear mixed models to mass-univariate
data using the lme tools in matlab.
I am currently trying to compute the initial vertex-wise temporal
covariance estimates by [lhTh0lhRe] =
lme_mass_fit_EMinit(X,[2],ni,lhcortex,3]
However, I keep getting this error message:
Undefined function 'matlabpool' for input arguments of type 'char'.
Error in lme_mass_fit_init (line 74)
if (prs==1) || (matlabpool('size') ~= prs)
Error in lme_mass_fit_EMinit (line 69)
[Theta1,Re1] = lme_mass_fit_init(X,Zcols,Y,ni,[],prs);
I have defined X, Y etc according to the previous steps available on
the wiki. Would be very grateful for any clarification on why this
error message keeps coming up.
Thank you very much,
Cathy
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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[Freesurfer] IOError: [Errno 13] Permission denied: 'aseg_stats.txt'
Dear FS team, I tried to run this command asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt But got this error,permission denied, SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Building the table.. Writing the table to aseg_stats.txt Traceback (most recent call last): File /usr/local/freesurfer/bin/asegstats2table, line 517, in module write_table(options, rows, columns, table) File /usr/local/freesurfer/bin/asegstats2table, line 462, in write_table tw.write() File /usr/local/freesurfer/bin/datastruct_utils.py, line 58, in write fp = open(self.filename, 'w') IOError: [Errno 13] Permission denied: 'aseg_stats.txt' freesurfer@freesurfer-VirtualBox:/usr/lib$ Many thanks Chikku ___ 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] Interior white matter surfaces
Dear FreeSurfer Experts, I am attempting to construct surfaces that are 1, 2, 3, and 4 mm interior from the GM/WM boundary (?h.white). So going gradually deeper into white matter from the GM/WM boundary. I have successfully used mris_fill to fill the ?h.white surface and mri_morphology to erode the resulting volume, but I'm not sure on the correct procedure to create the new surfaces. Any advice or suggestions on tools with options to use will be greatly appreciated! My eventual goal is to project coregistered DTI data onto these more interior white matter surfaces. Thanks! -Jason -- Jason Reed VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2946 Fax: (858) 642-3836 jr...@vapop.ucsd.edu ___ 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 MRIthickenThinWMStrands
Hi ERROR: MRIthickenThinWMStrands: invalid x,y,z! Numerical result out of range Any tips? S ___ 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] IOError: [Errno 13] Permission denied: 'aseg_stats.txt'
Hi Chikku, I think this is a permissions issue. Check that you have write permissions to where you are trying to write the stats table. -Louis On Wed, 19 Jun 2013, Varghese Chikku wrote: Dear FS team, I tried to run this command asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt But got this error,permission denied, SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Building the table.. Writing the table to aseg_stats.txt Traceback (most recent call last): File /usr/local/freesurfer/bin/asegstats2table, line 517, in module write_table(options, rows, columns, table) File /usr/local/freesurfer/bin/asegstats2table, line 462, in write_table tw.write() File /usr/local/freesurfer/bin/datastruct_utils.py, line 58, in write fp = open(self.filename, 'w') IOError: [Errno 13] Permission denied: 'aseg_stats.txt' freesurfer@freesurfer-VirtualBox:/usr/lib$ Many thanks Chikku ___ 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] Interior white matter surfaces
Hi Jason you could try using mris_expand with a negative # of millimeters. At 4mm you will lose a lot of the gyri and the procedure will probably fail, but for smaller amounts it should work (and is what we've done in the past). You can also use mris_distance_transform to compute the distance transform for the wm and use negative distances to find the distance into the interior cheers Bruce On Wed, 19 Jun 2013, Jason Reed wrote: Dear FreeSurfer Experts, I am attempting to construct surfaces that are 1, 2, 3, and 4 mm interior from the GM/WM boundary (?h.white). So going gradually deeper into white matter from the GM/WM boundary. I have successfully used mris_fill to fill the ?h.white surface and mri_morphology to erode the resulting volume, but I'm not sure on the correct procedure to create the new surfaces. Any advice or suggestions on tools with options to use will be greatly appreciated! My eventual goal is to project coregistered DTI data onto these more interior white matter surfaces. Thanks! -Jason ___ 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] Segmentation of MR-PET structurals
Hi Gabriel can you give us details of your acquisition? Why is it so noisy? Bruce On Wed, 19 Jun 2013, Gabriel Obregon wrote: Hi Douglas, The brainmask volumes are extremely grainy (similar to the raw structurals), i.e., dark voxels throughout the WM and high-intensity voxels across the gray matter. As far as I understood, all WM voxels (unless a lesion is present) should have a uniform intensity distribution after the normalization stages within the volume processing pipeline. Moreover, this makes the WM edits particularly challenging, for it's very difficult to trace the boundaries of some of the WM strands. I don't know if this represents an issue but it's definitely something I hadn't encountered before. Any input would be really appreciated! Thanks, --G On Jun 19, 2013, at 2:23 AM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Gabriel, I don't have experience with the MR-PET yet. Why do you think there is a problem? Try running wm-anat-snr on this subject. In general, you don't want to be smoothing/denoising the anatomical doug On 6/18/13 1:13 PM, obre...@nmr.mgh.harvard.edu wrote: Hi, I've started segmenting several structural scans from an MR-PET study conducted in Bay 7, and was wondering if someone has previous experience working with MPRAGE images acquired using the MR-PET coils? The scans have a very low SNR and I am trying to figure out if this could potentially affect the performance of the automated surface reconstructions. I've scrolled through the volumes and even though the surfaces seem normal, I am somewhat skeptical about their true quality given that intermediate stages, such as the intensity normalization, seem to be failing (please find an example from one of the brain masks attached). Is it essential to filter the raw structurals before segmenting them, and if so, are there any readily available denoising tools? Furthermore, are there any additional issues I should take into consideration? Thanks for your help! Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 MRIthickenThinWMStrands
nope, never seen that error. Probably from mri_segment. If you send me the input volume I'll take a look (check the recon-all.log and see what command was running when that happened). Also, definitely check it before sending to make sure it's reasonable On Wed, 19 Jun 2013, Sudhin A. Shah wrote: Hi ERROR: MRIthickenThinWMStrands: invalid x,y,z! Numerical result out of range Any tips? S ___ 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] MRIread.m and hippocampal subfields
Hi, Doug
Hi, all
This single BASH script line works like a charm for all posterior.mgz
files in a once and keeps the original names (must be in yoursubject/mri
folder).
for f in $(ls posterior*.mgz); do mri_convert -tr 0 -ti 0 -te 0
-flip_angle 0 -i $f -o $f; done
You can also use in a more complete script like:
#!/bin/bash
#usage myrecon subj (for example, myrecon bert)
mkdir ~/freesurfer/subjects/$1/mri/orig -p
cp ~/freesurfer/ImgOrig/$1/* ~/freesurfer/subjects/$1/mri/orig/
recon-all -all -s $1 -cw256 -hippo-subfields -qcache
cd ~/freesurfer/subjects/$1/mri
for f in $(ls posterior*.mgz); do mri_convert -tr 0 -ti 0 -te 0
-flip_angle 0 -i $f -o $f; done
This way all files will be fixed just after usual recon-all pipeline.
Notice you may adapt for your environment and recon-all options. Also,
ImgOrig is a custom folder where I have 1 folder for each of my subjects
with their respective images already prepared as 00x.mgz.
I hope you think it is useful.
BTW, I had to specify -i and -o in the command line. Using just the name
of the files did not work.
Thank you again, Doug.
Marcos
Em Ter, 2013-06-18 às 23:45 -0700, Douglas Greve escreveu:
Hi Marcos, it is weird that the posterior*.mgz does not have that
info. Maybe Koen or Eugenio know why. In the mean time, you can use
mri_convert to change/set the parameters, eg
mri_convert in.mgz out.mgz -tr 0 -ti 0 -te 0 -flip_angle 0
doug
On 6/18/13 2:50 PM, Marcos Martins da Silva wrote:
Hi, Freesurfer experts
If you try to read one of the posterior*.mgz files generated by
reco-all -hippo-subfield into MatLab/Octave using MRIread.m it fails
like this:
Ps=MRIread('posterior_left_subiculum.mgz')
WARNING: error reading MR params
Attempted to access mr_parms(1); index out of bounds because
numel(mr_parms)=0.
Error in MRIread (line 100)
tr = mr_parms(1);
That is because the posterior*.mgz files does not have this data. I
made a creating a little customized nMRIread.m with the following
changes:
if numel(mr_parms) 0
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
else
mr_parms(1) = 0;
mr_parms(2) = 0;
mr_parms(3) = 0;
mr_parms(4) = 0;
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
end
That works but it is only a quick workaround since MRIread,m calls
load_mgh.m and it shows a warning message about the mr_parms. This
message does not block my work but it is not good to see the warning
all the time on my screen. Perhaps the best fix would be just
creating the posterior*.mgz files with these data defined as 0. But
I would be happy if I could just edit these files defining these
values. Is there a freesurfer tool to make this simple edition? I
noticed, for example, that when you use mri_concat to sum these
files the resulting concatenated file is fixed and these parameters
are defined.
Thanks in advance,
Marcos.
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[Freesurfer] check orientation
Dear Freesurfer experts, is there a command in Freesurfer to check for correct orientation (LAS vs. PSR) of T1 images (similar to fslhd in FSL)? Thank you very much! Brigitte ___ 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] check orientation
Hi Brigette, not sure how you could do this except visually. Bring the images up and verify that the directions that we specify are correct (although of course this isn't possible for L/R unless you have some type of external fiducial marker like a vitamin E tablet) cheers Bruce On Wed, 19 Jun 2013, Brigitte Dahmen wrote: Dear Freesurfer experts, is there a command in Freesurfer to check for correct orientation (LAS vs. PSR) of T1 images (similar to fslhd in FSL)? Thank you very much! Brigitte ___ 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] export the ROIs in 'Desikan-Killiany' cortical atlas
Hi FreeSurfer expert, I am interested in a particular region of the Desikan-Killiany atlas and I'd like to use it as an ROI image mask in my fMRI analysis. Could you please suggest how I can do that? From here (http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation), I see that the DK atlas files are located here: $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs Question 1: how can I read this GCS file? Question 2: After I read this GCS file, how can I create an ROI image mask? I am thinking to use the WFU PickAtlas to create an ROI (http://fmri.wfubmc.edu/software/PickAtlas). Would it be a good fit? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] problem bbregister onto longitudinal pipeline
Hi Daniel, bbregister is completely independent of the longitudinal stream, so if it fails, it has other reasons (e.g. bad initial alignment). You could try to switch the initial alignment to some other methods. Best, Martin On Jun 14, 2013, at 3:25 AM, Daniel Garcia d.garcia-...@icm-institute.org wrote: Dear Freesurfer Users, I'm having a problem to register my PET images into the longitudinal pipeline of freesurfer (version 5.1). I have use bbregister without any problem to put the PET image into the crossectional images but it fails to register to the long version of it. Someone can tell me if I'm doing something wrong? bbregister -s P09_TA --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz This last command works perfectly, but bbregister -s P09_TA.long.P09 --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz Fails completely. My objective is to project my pet cortex into the surface in longitudinal that is why I'm interested in this processing. Maybe you can tell my another way of doing this. Thank you very much. Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Dr. Martin Reuter 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 ___ 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 --qdec long
Hi Catherine, probably you are not using 5.3. otherwise it should recognize the --qdec-long flag. You can open mris_preproc and take a look (it is a text file), there should be a qdec-long if you search it. Best, Martin On Jun 17, 2013, at 12:04 PM, Catherine Bois c.b...@sms.ed.ac.uk wrote: Dear Freesurfer experts, I am trying to prepare my data for linear mixed modeling using the matlab add ons, with this command mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh However I keep getting this error message ERROR: flag --qdec-long not recognized I am using version 5.3 and read on the release notes that qdec-long only works with unix input text files (\n newline). I thought that was the format of my textfile, and also confused as to why the wrong format of the file would make the flag unrecognized as opposed to the textfile...I was also wondering whether the -long table needs to be shrunk to cross-sectional format as it does in the two stage model? I have attached an excerpt of my textfile qdec, would greatly appreciate help in establishing whether it is somehow the format of the textfile that is the problem? Thank you very much for your help, Best Wishes, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. qdec.table.dat___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Dr. Martin Reuter 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 ___ 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 processing
Hi Linn, do you mean the brain mask in the cross sectional runs gets worse after you run the longitudinal steps (base and long)? That is not really possible, as these steps don't touch the cross data (only read from it). If you mean that the brain mask in the long looks worse than in the cross (of same subject time point), then you need to check the brain mask in the base. That one is copied to all the longitudinal runs, so it needs to be accurate in the base. If it is accurate there, but still not in a specific longitudinal run then that indicates a mis-alignment to the base. If that is the case, the first thing I'd try is rename base and all longitudinals and re-run those from scatch to make sure it's not a hick-up (e.g. io problem). Best, Martin On Jun 18, 2013, at 5:16 AM, Linn Mittlestein linnmit...@gmail.com wrote: Dear Freesurfer group. I am having some concerns about Freesurfer and the different steps. I have used version 5.0 for the cross-sectional timepoints, and I am now using version 5.3 for the longitudinal processing. I am doing therefore the several different steps involved in longitudinal processing, for example -base, -long runs and now for the lme analysis with matlab also the smoothing steps etc. I am very concerned however because looking at the brain masks after these steps have been done (ie the cross-sectional runs), they look much worse than they did before the longitudinal editing began; large chunks of surfaces are missing. Has anybody else reported this problem? Could it be because the longitudinal steps are now being done with version 5.3 as opposed to 5? Surely this should not have such a large effect on the brainmasks, as to completely deform them? Kind Regards, Linn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Dr. Martin Reuter 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 ___ 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.
