[Freesurfer] hippocampal subfield segmentations
I heard from Koen a while back that a new improved version was in the works. I have several projects I would be interested in using it for. Any info on timelines for release or a publication ? thank You ___ 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] Demean covariate
Dear Doug and Freesurfers, I noticed that the DOSS option no longer exists in qdec and that Doug said there was a bug related to it. If i want to assess the differences in cortical thickness between groups while covariating for age and gender, since i don't expect any interactions, can i just demean the covariates and make my analysis in qdec with dods? 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.
[Freesurfer] qdec.table.dat
Hello, Any help how to make qdec.table.dat file will be highly appreciated. Thanks Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqure...@gist.ac.kr URL : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to ___ 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] DOSS contrast - one group, 3 covariates
Hi everyone, I want to analyze with DOSS the relationship between performance on a cognitive task (called '15wt') and cortical thickness, in one group, controlling for the effects for age, gender and education. As a Freesurfer-newbie, it be would really great if someone could check my .sfgd file and contrast. .sfgd file: GroupDescriptorFile 1 Class .00 plus blue (this is the gender part) Class 1.00 plus red Variables 15_wt Age Edu Input 0050 .00 52 73 4 Input 0051 .00 38 68 5 Input 0054 1.00 35 57 4 Input 0060 1.00 46 58 6 Input 0062 1.00 46 45 5 etc. contrast: 0 0 .5 0 0 Is this correct? Thanks in advance! Anita ___ 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] FSL masks applied to Freesurfer surfaces?
Do you want to transfer them to fsaverage space or to the individual anatomical space? doug On 10/04/2013 01:42 AM, Ruth Carper wrote: Hi, I'd like to take some masks that I have in MNI standard space in FSL and map them to Freesurfer surface space. The goal is to extract measures of average cortical thickness (or area or etc) for those regions for each subject. Is there a standard way to do this? ___ 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] DOSS contrast - one group, 3 covariates
Yes, though I would probably use [0 0 1 0 0] instead of .5. They will give you identical p-values. Using 1 instead of .5 makes the beta value (ie, regresssion coefficient) more interpretable (if that is something you will look at). doug On 10/04/2013 07:50 AM, Anita van Loenhoud wrote: Hi everyone, I want to analyze with DOSS the relationship between performance on a cognitive task (called '15wt') and cortical thickness, in one group, controlling for the effects for age, gender and education. As a Freesurfer-newbie, it be would really great if someone could check my .sfgd file and contrast. .sfgd file: GroupDescriptorFile 1 Class .00 plus blue (this is the gender part) Class 1.00 plus red Variables 15_wt Age Edu Input 0050 .00 52 73 4 Input 0051 .00 38 68 5 Input 0054 1.00 35 57 4 Input 0060 1.00 46 58 6 Input 0062 1.00 46 45 5 etc. contrast: 0 0 .5 0 0 Is this correct? Thanks in advance! Anita ___ 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] qdec.table.dat
Have you looked atthe qdec tutorial? On 10/04/2013 05:41 AM, Muhammad Naveed Iqbal Qureshi wrote: Hello, Any help how to make qdec.table.dat file will be highly appreciated. Thanks *Best Regards,* *Muhammad Naveed Iqbal Qureshi* Ph.D. Candidate Bio-Medical Signal System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqure...@gist.ac.kr mailto:mniqure...@gist.ac.kr URL : http://bmssa.gist.ac.kr http://bmssa.gist.ac.kr/ Pplease don't print this e-mail unless you really need to ___ 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] Demean covariate
Demeaning will not turn a DODS into a DOSS. On 10/04/2013 04:48 AM, Erik Lindberg wrote: Dear Doug and Freesurfers, I noticed that the DOSS option no longer exists in qdec and that Doug said there was a bug related to it. If i want to assess the differences in cortical thickness between groups while covariating for age and gender, since i don't expect any interactions, can i just demean the covariates and make my analysis in qdec with dods? Thanks! ___ 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] Help with mri_copy_values
I'm trying to apply voxel deletions made to the brainmask.mgz to the wm.mgz. As I understand it, if I run mri_copy_values brainmask.mgz 0 wm.mgz all of the 0 value voxels, or the deleted voxels in braibmask.mgz will be applied to the wm.mgz (provided they have the same geometry or some such). it seems to run properly and says voxels copied from input to output volume but when I load in tkmedit or freeview the wm.mgz still contains voxels where there are none in the brainmask.mgz any ideas? jon ___ 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] Error when running mris_anatomical_stats
Hello Freesurfer experts, I am having difficulty when trying to extract LGI values from a specific label I made. mris_anatomical seems to work when I run it with an annotation, so I am not sure why I am having this error. mris_anatomical_stats -l sub200/label/lh.precuneus.label -t sub200/surf/lh.pial_lgi -f sub200/stats/lh.precuneus_lgi.stats sub200 lh This is the output: limiting computations to label sub200/label/lh.trait_precuneus.label. using thickness file sub200/surf/lh.pial_lgi. reading volume /media/LGI/LGI/sub200/mri/wm.mgz... reading input surface /media/LGI/LGI/sub200/surf/lh.white... reading input pial surface /media/LGI/LGI/sub200/surf/lh.pial... reading input white surface /media/LGI/LGI/sub200/surf/lh.white... Segmentation fault (core dumped) Thank you for the help! Tara ___ 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] Repost: pcc maps and mri_glmfit
Hi Doug, I guess it boils down to the question how to get a group PCC map after a RFX GLM? Using -m PCC seems to only give me a map per subject. Are you calculating PCC from the t- values? Thanks, Caspar On Thursday, October 3, 2013, Caspar M. Schwiedrzik wrote: Hi Doug, On Thursday, October 3, 2013, Douglas N Greve wrote: It sounds like two issues: 1. p-values not consistent with your program. What did you use to compute? Did you do a two-sided (which is what fsfast uses)? I used ttest in Matlab, two sided. 2. Using pcc maps. Why not use -m pcc? Isn't that giving me a map per subject? How do I get the group map that is consistent with the results of mri_glmfit run on ces.nii? Thanks, Caspar doug On 10/03/2013 01:10 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I loaded the pcc.nii file that I got from isxconcat-sess into Matlab and then ran a t-test against 0 over the 4th dimension. I converted the resulting p-values to -log10 and then compared them to the output of mri_glmfit, namely sig.vol. This was the mri_glmfit command: mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname I was expecting the p-values to be the same, which apparently is not the case, unless I am doing/understanding something wrong. By now, I am actually more inclined to use the regression coefficients instead. However, I'd still like to get pcc maps from them, if there is a way to do so in FSFAST. Thanks, Caspar 2013/10/3 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.edu On 10/03/2013 10:39 AM, Caspar M. Schwiedrzik wrote: Hi Doug, when I run a two-tailed t-test against 0 in Matlab on the Rs in pcc.nii that I get out of isxconcat-sess with -m pcc, and DOF from ffxdof.dat, I get different -log10(p) values than the ones that come out of mri_glmfit. I don't understand what you mean. Can you elaborate? I am not sure why this is happening. In principle, I just want pcc maps as final output to show them on the surface (instead of p-values). So I'd be happy to follow your advice regarding the biasing effects of noise and autocorrelation and use the regression coefficients. However, mri_glmfit (v5.1) does not seem to output pcc maps of the contrasts (contrary to selxavg3-sess on the single subject level). How would I get those? Thanks, Caspar 2013/10/1 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 On 10/01/2013 01:13 PM, Caspar M. Schwiedrzik wrote: Hi Doug, it would be great if you could give me some further advise on the group analysis of functional connectivity maps. Specifically, I am trying to get PCC maps for certain seeds, and am not planning any comparison between groups. Following your previous advise, I am running isxconcat-sess with -m pcc to get the PCC maps. I would then run mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname *Could you please provide some more detail on what kind of analysis is performed when I provide pcc.nii as an input for mri_glmfit? Is it a t-test of the Fisher-transformed r-values against 0? I just run a t-test of the r-values. I don't have a program to convert them to z-values, however, there are z-values that are created in the first level analysis. These are generated from the p-values but I bet it would give you the same thing. Use -m z with isxconcat-sess if you want to use the z. *Is the average r-value or z-value saved somewhere? Which level? For mri_glmfit, they are not, but it is not hard to get them with matlab. *Do you take the autocorrelation into account (as in Vincent JL et al., 2007. Intrinsic functional architecture in the anaesthetized monkey brain. Nature. 447:83-86)? Not usually, but it could be done by not including -no-whiten when you run mkanalysis-sess. I usually use the regression coefficients instead of correlation coefficients because that they are at least unbiased with respect to noise level and autocorrelation. doug I'd also be happy to look this up but
[Freesurfer] Cluster Annotation file and mris_anatomical_stats
Hi Everyone,
I am having trouble running mris_anatomical_stats on an annotation file
produced from my group analysis in qdec.
This is my code, but it seems to want to pull the annotation file from the
subject/label directory. Should I just make a copy into everyone's label file?
mris_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot -t
${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
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Re: [Freesurfer] Repost: pcc maps and mri_glmfit
I think you are conflating the 1st level and the 2nd level. You could get pcc out of the 2nd level regardless of what you are using for the input from the first level. I've attached a matlab script that will compute the pcc for mri_glmfit output doug On 10/04/2013 03:33 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I guess it boils down to the question how to get a group PCC map after a RFX GLM? Using -m PCC seems to only give me a map per subject. Are you calculating PCC from the t- values? Thanks, Caspar On Thursday, October 3, 2013, Caspar M. Schwiedrzik wrote: Hi Doug, On Thursday, October 3, 2013, Douglas N Greve wrote: It sounds like two issues: 1. p-values not consistent with your program. What did you use to compute? Did you do a two-sided (which is what fsfast uses)? I used ttest in Matlab, two sided. 2. Using pcc maps. Why not use -m pcc? Isn't that giving me a map per subject? How do I get the group map that is consistent with the results of mri_glmfit run on ces.nii? Thanks, Caspar doug On 10/03/2013 01:10 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I loaded the pcc.nii file that I got from isxconcat-sess into Matlab and then ran a t-test against 0 over the 4th dimension. I converted the resulting p-values to -log10 and then compared them to the output of mri_glmfit, namely sig.vol. This was the mri_glmfit command: mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname I was expecting the p-values to be the same, which apparently is not the case, unless I am doing/understanding something wrong. By now, I am actually more inclined to use the regression coefficients instead. However, I'd still like to get pcc maps from them, if there is a way to do so in FSFAST. Thanks, Caspar 2013/10/3 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu On 10/03/2013 10:39 AM, Caspar M. Schwiedrzik wrote: Hi Doug, when I run a two-tailed t-test against 0 in Matlab on the Rs in pcc.nii that I get out of isxconcat-sess with -m pcc, and DOF from ffxdof.dat, I get different -log10(p) values than the ones that come out of mri_glmfit. I don't understand what you mean. Can you elaborate? I am not sure why this is happening. In principle, I just want pcc maps as final output to show them on the surface (instead of p-values). So I'd be happy to follow your advice regarding the biasing effects of noise and autocorrelation and use the regression coefficients. However, mri_glmfit (v5.1) does not seem to output pcc maps of the contrasts (contrary to selxavg3-sess on the single subject level). How would I get those? Thanks, Caspar 2013/10/1 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 On 10/01/2013 01:13 PM, Caspar M. Schwiedrzik wrote: Hi Doug, it would be great if you could give me some further advise on the group analysis of functional connectivity maps. Specifically, I am trying to get PCC maps for certain seeds, and am not planning any comparison between groups. Following your previous advise, I am running isxconcat-sess with -m pcc to get the PCC maps. I would then run mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname *Could you please provide some more detail on what kind of analysis is performed when I provide pcc.nii as an input for mri_glmfit? Is it a t-test of the Fisher-transformed r-values
[Freesurfer] Global thickness calculation
Hi, I am trying to calculate whole-brain mean cortical thickness in each individual subject for correction of regional mean thicknesses. I see on the wiki that this is recommended to be done by: bh.thickness = (lh.thickness X lh.area) + (rh.thickness X rh.area) / (lh.area +rh.area) In my table I see lh and rh total area but I do not see lh and rh thickness. All I see is mean thicknesses for each region. Are the total rh and lh mean thicknesses supposed to appear in the table? 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] mris_smooth issue with gaussian parameters
how long have you waited? On Fri, 4 Oct 2013, Marcos Martins da Silva wrote: Hi, Freesurfers I am getting some interesting hippocampal surfaces with the following steps: 1- recon-all -all -hippo-subfields 2- mri-concat (only CA1, CA23, CA4DG and the tail complement volumes) 3- a custom OCTAVE script to segment the concatenated volume from step 2 into Head, Body and Tail 4- mri_binarize Head, Body and Tail volumes from step 3 5- mri_tessellate the binary masks from step 4 6- mri_smooth the surfaces from step 5 Using freeview I got a screenshot showing both hippocampi segmented (hipposurf3d.png is attached). This approach worked well for 16 subjects up to step 5. Step 6 was completed as well in 13 out 16 subjects. The only problem was during left hippocampal body smoothing in 3 subjects (all the other surfaces from all 16 subjects in were smoothed with no problem). For these 3 surfaces, mris_smooth simply freezes, with no error message. I must press control + C to quit the program. During the freezing I noticed high CPU use. It follows the exactly command I used and the screen output. mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoBody lh.surfHippoBody using Gaussian curvature smoothing with norm 5.00 with 2 smooth steps averaging curvature for 1 iterations smoothing for 1 iterations smoothing surface tessellation for 1 iterations... -- -- -- pass 1 (num=2853) -- -- -- If I supress the gaussian parameters and run just something like: mris_smooth -nw -a 1 -n 1 surfLeftHippoBody lh.surfHippoBody or even mris_smooth -nw surfLeftHippoBody lh.surfHippoBody I got the smoothed surface with no errors but the final quality is not as good as when I use the gaussian parameters. I am attaching one of the problematic surface files so you can check it (surfLeftHippobody). Intersting if I use a surface with all left hippocampus (including head, problematic body and tail and) smoothing completes without error Thank you very much for any help. Marcos ___ 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] MPRAGE SNR
Dear FreeSurfer Experts, Is there a way to estimate the SNR in MPRAGE scans besides using wm-anat-snr ? For examples, I read that SNR is improved in multiecho MPRAGE and I am wondering how that is computed? Thanks! Daniel ___ 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 longitudinal data
That command works. Thanks so much, Martin! Best, Tricia From: Martin Reuter mreu...@nmr.mgh.harvard.edu To: Tricia Merkley tmerkl...@yahoo.com Cc: Freesurfer list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 3, 2013 9:48 AM Subject: Re: [Freesurfer] LGI longitudinal data Hi Tricia, try recon-all -long subject001 subject001_base -localGI Best, Martin On 09/28/2013 01:53 PM, Tricia Merkley wrote: Hi, Is it possible to run the LGI on data that has already been longitudinally processed? For example, when I try to run: recon-all -s subject001.long.subject001_base -localGI I get the following error: ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters: \' -long tpNid templateid \' where tpNid is the time point id (SAME as cross sectional ID) and templateid is the ID created in the -base run. The directory tpNid.long.templateid will be created automatically or used for output, if it already exists. This is using v5.1.0, and no, I'm not trying to re-run a longitudinal time point. Just the LGI. I'd appreciate any suggestions! Thanks so much, Tricia ___ 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] Repost: pcc maps and mri_glmfit
Can you tar up you glmfit dir and drop it to me on our file drop? On 10/04/2013 05:29 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thank you very much for sending the Matlab function. When I run this, it creates a pcc.mgh file for my osgm contrast. However, the values seem strange. They range from -630 to 36 for my particular dataset. I was expecting something between -1 and 1. Caspar 2013/10/4 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu I think you are conflating the 1st level and the 2nd level. You could get pcc out of the 2nd level regardless of what you are using for the input from the first level. I've attached a matlab script that will compute the pcc for mri_glmfit output doug On 10/04/2013 03:33 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I guess it boils down to the question how to get a group PCC map after a RFX GLM? Using -m PCC seems to only give me a map per subject. Are you calculating PCC from the t- values? Thanks, Caspar On Thursday, October 3, 2013, Caspar M. Schwiedrzik wrote: Hi Doug, On Thursday, October 3, 2013, Douglas N Greve wrote: It sounds like two issues: 1. p-values not consistent with your program. What did you use to compute? Did you do a two-sided (which is what fsfast uses)? I used ttest in Matlab, two sided. 2. Using pcc maps. Why not use -m pcc? Isn't that giving me a map per subject? How do I get the group map that is consistent with the results of mri_glmfit run on ces.nii? Thanks, Caspar doug On 10/03/2013 01:10 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I loaded the pcc.nii file that I got from isxconcat-sess into Matlab and then ran a t-test against 0 over the 4th dimension. I converted the resulting p-values to -log10 and then compared them to the output of mri_glmfit, namely sig.vol. This was the mri_glmfit command: mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname I was expecting the p-values to be the same, which apparently is not the case, unless I am doing/understanding something wrong. By now, I am actually more inclined to use the regression coefficients instead. However, I'd still like to get pcc maps from them, if there is a way to do so in FSFAST. Thanks, Caspar 2013/10/3 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 On 10/03/2013 10:39 AM, Caspar M. Schwiedrzik wrote: Hi Doug, when I run a two-tailed t-test against 0 in Matlab on the Rs in pcc.nii that I get out of isxconcat-sess with -m pcc, and DOF from ffxdof.dat, I get different -log10(p) values than the ones that come out of mri_glmfit. I don't understand what you mean. Can you elaborate? I am not sure why this is happening. In principle, I just want pcc maps as final output to show them on the surface (instead of p-values). So I'd be happy to follow your advice regarding the biasing effects of noise and autocorrelation and use the regression coefficients. However, mri_glmfit (v5.1) does not seem to output pcc maps of the contrasts (contrary to selxavg3-sess on the single subject level). How would I get those? Thanks, Caspar 2013/10/1 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
Re: [Freesurfer] Global thickness calculation
you can do something like this cd $SUBJECTS_DIR/$subject mri_segstats --slabel $subject lh label/lh.cortex.label --i surf/lh.thickness --id 1 --sum stats/lh.meanthickness.dat On 10/04/2013 05:22 PM, Mollie Bayda wrote: Hi, I am trying to calculate whole-brain mean cortical thickness in each individual subject for correction of regional mean thicknesses. I see on the wiki that this is recommended to be done by: bh.thickness = (lh.thickness X lh.area) + (rh.thickness X rh.area) / (lh.area +rh.area) In my table I see lh and rh total area but I do not see lh and rh thickness. All I see is mean thicknesses for each region. Are the total rh and lh mean thicknesses supposed to appear in the table? Thanks! ___ 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] Cluster Annotation file and mris_anatomical_stats
This may sound incredibly trivial, but try putting a ./ infront of
qdec, ie, -a ./qdec/...
doug
On 10/04/2013 03:42 PM, Tara Ann Miskovich wrote:
Hi Everyone,
I am having trouble running mris_anatomical_stats on an annotation file
produced from my group analysis in qdec.
This is my code, but it seems to want to pull the annotation file from the
subject/label directory. Should I just make a copy into everyone's label file?
mris_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
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--
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/
___
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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] Repost: pcc maps and mri_glmfit
Done. Thank you very much for looking into this. Caspar 2013/10/4 Douglas N Greve gr...@nmr.mgh.harvard.edu Can you tar up you glmfit dir and drop it to me on our file drop? On 10/04/2013 05:29 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thank you very much for sending the Matlab function. When I run this, it creates a pcc.mgh file for my osgm contrast. However, the values seem strange. They range from -630 to 36 for my particular dataset. I was expecting something between -1 and 1. Caspar 2013/10/4 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu I think you are conflating the 1st level and the 2nd level. You could get pcc out of the 2nd level regardless of what you are using for the input from the first level. I've attached a matlab script that will compute the pcc for mri_glmfit output doug On 10/04/2013 03:33 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I guess it boils down to the question how to get a group PCC map after a RFX GLM? Using -m PCC seems to only give me a map per subject. Are you calculating PCC from the t- values? Thanks, Caspar On Thursday, October 3, 2013, Caspar M. Schwiedrzik wrote: Hi Doug, On Thursday, October 3, 2013, Douglas N Greve wrote: It sounds like two issues: 1. p-values not consistent with your program. What did you use to compute? Did you do a two-sided (which is what fsfast uses)? I used ttest in Matlab, two sided. 2. Using pcc maps. Why not use -m pcc? Isn't that giving me a map per subject? How do I get the group map that is consistent with the results of mri_glmfit run on ces.nii? Thanks, Caspar doug On 10/03/2013 01:10 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I loaded the pcc.nii file that I got from isxconcat-sess into Matlab and then ran a t-test against 0 over the 4th dimension. I converted the resulting p-values to -log10 and then compared them to the output of mri_glmfit, namely sig.vol. This was the mri_glmfit command: mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname I was expecting the p-values to be the same, which apparently is not the case, unless I am doing/understanding something wrong. By now, I am actually more inclined to use the regression coefficients instead. However, I'd still like to get pcc maps from them, if there is a way to do so in FSFAST. Thanks, Caspar 2013/10/3 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu On 10/03/2013 10:39 AM, Caspar M. Schwiedrzik wrote: Hi Doug, when I run a two-tailed t-test against 0 in Matlab on the Rs in pcc.nii that I get out of isxconcat-sess with -m pcc, and DOF from ffxdof.dat, I get different -log10(p) values than the ones that come out of mri_glmfit. I don't understand what you mean. Can you elaborate? I am not sure why this is happening. In principle, I just want pcc maps as final output to show them on the surface (instead of p-values). So I'd be happy to follow your advice regarding the biasing effects of noise and autocorrelation and use the regression coefficients. However, mri_glmfit (v5.1) does not seem to output pcc maps of the contrasts (contrary to selxavg3-sess on the single subject level). How would I get those?
Re: [Freesurfer] Error when running mris_anatomical_stats
Hi Tara if you upload the subject we will track it down cheers Bruce On Fri, 4 Oct 2013, Tara Ann Miskovich wrote: Hello Freesurfer experts, I am having difficulty when trying to extract LGI values from a specific label I made. mris_anatomical seems to work when I run it with an annotation, so I am not sure why I am having this error. mris_anatomical_stats -l sub200/label/lh.precuneus.label -t sub200/surf/lh.pial_lgi -f sub200/stats/lh.precuneus_lgi.stats sub200 lh This is the output: limiting computations to label sub200/label/lh.trait_precuneus.label. using thickness file sub200/surf/lh.pial_lgi. reading volume /media/LGI/LGI/sub200/mri/wm.mgz... reading input surface /media/LGI/LGI/sub200/surf/lh.white... reading input pial surface /media/LGI/LGI/sub200/surf/lh.pial... reading input white surface /media/LGI/LGI/sub200/surf/lh.white... Segmentation fault (core dumped) Thank you for the help! Tara ___ 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] Help with mri_copy_values
Hi Jon voxels deleted with tkmedit are set to 1, not 0, so try that Bruce On Fri, 4 Oct 2013, Jonathan Holt wrote: I'm trying to apply voxel deletions made to the brainmask.mgz to the wm.mgz. As I understand it, if I run mri_copy_values brainmask.mgz 0 wm.mgz all of the 0 value voxels, or the deleted voxels in braibmask.mgz will be applied to the wm.mgz (provided they have the same geometry or some such). it seems to run properly and says voxels copied from input to output volume but when I load in tkmedit or freeview the wm.mgz still contains voxels where there are none in the brainmask.mgz any ideas? jon ___ 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.
