[Freesurfer] contrast matrix
Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: genotype with three levels (GG,GA,AA ); gender (F, M), and one covariate. So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA. 1) I want to perform the difference between any of the genotype leves analysis with regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: [1 -1 0 1 -1 0 0 0 0 0 0 0 ]/2 [1 0 -1 1 0 -1 0 0 0 0 0 0 ]/2 is it correct? Any help will be very appreciated. Best wishes, Meng Li ___ 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] contrast matrix
Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: genotype with three levels (GG,GA,AA ); gender (F, M), and one covariate. So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA. 1) I want to perform the difference between any of the genotype leves analysis with regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: [1 -1 0 1 -1 0 0 0 0 0 0 0 ]/2 [1 0 -1 1 0 -1 0 0 0 0 0 0 ]/2 is it correct? Any help will be very appreciated. Best wishes, Bo Xiang ___ 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 in analyze command failed: mri_concat
Hello Freesurfer experts, I have got some problems with qdec. For testing my data i make an design with age, sexe and right and left hippocampus. The same design as the tutorial on the freesurfer wiki. When starting anlalyze i get an Error in Analyze: command failed: mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh. surf is the map with the smoothings. The correct smoothings file. In this design is 10 is correctly presented in the map surf. Thanks, Stan lh-Avg-Intercept-volume --- Does the average volume differ from zero? 1.000 1.000 0.000 0.000; lh-Avg-volume-Left-Hippocampus-Cor --- Does the correlation between volume and Left-Hippocampus, accounting for gender, differ from zero? 0.000 0.000 1.000 1.000; lh-Diff-male-female-Intercept-volume --- Does the average volume differ between male and female? 1.000 -1.000 0.000 0.000; lh-Diff-male-female-Cor-volume-Left-Hippocampus --- Does the volume--Left-Hippocampus correlation differ between male and female? 0.000 0.000 1.000 -1.000; ninputs = 9 Checking inputs reading MRI_FRAME structure from file... Error in Analyze: command failed: mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh lh-Avg-Intercept-volume --- Does the average volume differ from zero? 1.000 1.000 0.000 0.000; lh-Avg-volume-Left-Hippocampus-Cor --- Does the correlation between volume and Left-Hippocampus, accounting for gender, differ from zero? 0.000 0.000 1.000 1.000; lh-Diff-male-female-Intercept-volume --- Does the average volume differ between male and female? 1.000 -1.000 0.000 0.000; lh-Diff-male-female-Cor-volume-Left-Hippocampus --- Does the volume--Left-Hippocampus correlation differ between male and female? 0.000 0.000 1.000 -1.000; ninputs = 9 Checking inputs reading MRI_FRAME structure from file... Error in Analyze: command failed: mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh Type: Error Time: Tue Nov 13 11:57:43 2012 Description: Error in Analyze: command failed: mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh Type: Error Time: Tue Nov 13 11:45:07 2012 Description: Error in Analyze:
[Freesurfer] Phase Encoding Direction and epidewarp.fsl
Hi everyone, I recently switched the phase encoding direction of the functional sequence I've been using from F H to R L and ran into a problem with epidewarp.fsl (in version 4). The unwarping was still happening along the F H axis in the new images where phase encoding was R L. (Note: I'm working with NHPs in sphinx position, but I'll describe my problem in standard coordinates to keep everything somewhat simpler) Because thought that epidewarp.fsl might be having a difficult time determining the phase encoding direction, I swapped the position of the F H and R L dimensions in my nifti file (going from LIP to IRP) and the dewarping now seems to work. Is there something going wrong in the unpacking such that the phase encoding information is lost? Also, is the phase encoding information stored anywhere in the nifti, so that I can automatically detect and correct cases like this? Thanks for the help, Clark ___ 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] bankssts label
Dear Freesurfers, Does anyone know why sometimes the bankssts (banks of the superior temporal sulcus) is only found in the sulcus, and sometimes occupies a sizeable part of an adjacent gyrus (superior temporal / inferior parietal)? The dark-green area is generally only visible in the inflated view, but every so often it is quite pronounced in the main (pial) view as well. Thanks! Vincent Mensen Utrecht -- De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. -- This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this 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] segmentation problem.
the intensity normalization has a region growing component that is bounded by intensity gradients. In images like MPRAGE, where SNR is traded for CNR it can help to raise the threshold for stopping so that more white matter is included (that's what the -b 20 does, I think the default it 10 or 15). This is usually not good for SPGR/FLASH and can result in the region growing escaping the white matter and eroding the gray matter, which looks like it happened in your case. cheers Bruce On Tue, 13 Nov 2012, youngmin huh wrote: Thanks. I'll try without expert opts.But i'm not sure if i can get better results. Before I found out these expert opts, I ran some images recon2 without expert opts. And they got poor segmentation. Actually, some images showed improvement with those options. I'm curious why these options work for some images and don't for others. And, 3D SPGR sequences were used. (TR=22, TE=4, thickness=1.4, FOV=240*240, FA=40) 2012/11/12 Bruce Fischl fis...@nmr.mgh.harvard.edu Can you try it without the expert opts? And what sequence is the data? On Nov 12, 2012, at 3:35 AM, youngmin huh ymin1...@gmail.com wrote: Hi I'm working with some images, and freesurfer didn't properly detect some of their white matter boundaries. I attached some examples. I ran recon2 with expert options(-b 20 -n 5). As you can see, they have inaccurate white matter boundaries in curved area. I think it's not that highly curved, though. Any comment will be appreciated. Thanks, Youngmin Huh image.jpegimage.jpeg ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] bad acquisition and noise problem.
what is the bandwidth? The typical way to fix it is to increase the bandwidth. You can probably recover some of the SNR you will lose by reducing your flip angle, which is pretty far from the Ernst angle. Also, minimize your TE (if 4ms is not already the min) cheers Bruce On Tue, 13 Nov 2012, youngmin huh wrote: Hi, 3D SPGR sequences were used. (TR=22, TE=4, thickness=1.4, FOV=240*240, FA=40) If the artifacts are due to B0 distortion, I wonder how I can fix it. Thanks, Youngmin Huh 2012/11/12 Bruce Fischl fis...@nmr.mgh.harvard.edu Can you give us the acquisition details? I suspect this is not noise, but rather B0 distortion. what is the acquisition? And what bandwidth? On Nov 8, 2012, at 2:53 AM, youngmin huh ymin1...@gmail.com wrote: Dear all, I'm working with some images, and they have so much noises on temporal areas. I just ran recon2, but not sure if they'll be segmented properly. Does anyone have a recommendation for dealing with it? I wonder if there is any flag or option for this occasion. I would appreciate any comments or help. I attached an example. Thanks, Youngmin Huh temporal_001.jpg 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
[Freesurfer] gstro...@ggmail.com, analysis-b...@nmr.mgh.harvard.edu
Hi Freesurferers or Experts, I have been trying to convert the watershed bem brain surfaces to vol with mri_fill and mri_surf2vol but not succeed. My main aim is to create mask for outer_skull, inner_skull and other from their respective surfaces. Is there any other method to use? Azeez Azeez Adebimpe ___ 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] Phase Encoding Direction and epidewarp.fsl
Hi Clark, the phase encode direction is always lost since that information is not represented in the nifti header. epidewarp.fsl always assumes that the phase encode direction is in the row direction. doug On 11/13/2012 07:32 AM, Clark Fisher wrote: Hi everyone, I recently switched the phase encoding direction of the functional sequence I've been using from F H to R L and ran into a problem with epidewarp.fsl (in version 4). The unwarping was still happening along the F H axis in the new images where phase encoding was R L. (Note: I'm working with NHPs in sphinx position, but I'll describe my problem in standard coordinates to keep everything somewhat simpler) Because thought that epidewarp.fsl might be having a difficult time determining the phase encoding direction, I swapped the position of the F H and R L dimensions in my nifti file (going from LIP to IRP) and the dewarping now seems to work. Is there something going wrong in the unpacking such that the phase encoding information is lost? Also, is the phase encoding information stored anywhere in the nifti, so that I can automatically detect and correct cases like this? Thanks for the help, Clark ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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 in analyze command failed: mri_concat
Hi Stan, can you run that mri_concat command from the terminal command line and send me the resulting terminal output? I've put the command below doug mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh On 11/13/2012 06:53 AM, Berg, S.F. van den wrote: mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Phase Encoding Direction and epidewarp.fsl
hi doug, just to follow up on this. if i had the phase encode direction (we currently store various dicom attributes in a nifti header extension), where would i provide it? cheers, satra On Tue, Nov 13, 2012 at 11:27 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Clark, the phase encode direction is always lost since that information is not represented in the nifti header. epidewarp.fsl always assumes that the phase encode direction is in the row direction. doug On 11/13/2012 07:32 AM, Clark Fisher wrote: Hi everyone, I recently switched the phase encoding direction of the functional sequence I've been using from F H to R L and ran into a problem with epidewarp.fsl (in version 4). The unwarping was still happening along the F H axis in the new images where phase encoding was R L. (Note: I'm working with NHPs in sphinx position, but I'll describe my problem in standard coordinates to keep everything somewhat simpler) Because thought that epidewarp.fsl might be having a difficult time determining the phase encoding direction, I swapped the position of the F H and R L dimensions in my nifti file (going from LIP to IRP) and the dewarping now seems to work. Is there something going wrong in the unpacking such that the phase encoding information is lost? Also, is the phase encoding information stored anywhere in the nifti, so that I can automatically detect and correct cases like this? Thanks for the help, Clark ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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 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] contrast matrix
That contrast will do what you want but a more general one would be [1 -1 0 0 0 0 0 0 0 0 0 0] [0 0 0 1 -1 0 0 0 0 0 0 0] [1 0 -1 0 0 0 0 0 0 0 0 0] [0 0 0 1 0 -1 0 0 0 0 0 0] This will return positive if there is any difference between the genotypes regardless of gender. In your contrast, you could have a situation where the G-A difference is positive for males but negative for females in which case they would cancel each other out. doug On 11/13/2012 08:50 AM, xiangbo_2010 wrote: Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: genotype with three levels (GG,GA,AA ); gender (F, M), and one covariate. So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA. 1) I want to perform the difference between any of the genotype leves analysis with regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: [1 -1 0 1 -1 0 0 0 0 0 0 0 ]/2 [1 0 -1 1 0 -1 0 0 0 0 0 0 ]/2 is it correct? Any help will be very appreciated. Best wishes, Bo Xiang -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Phase Encoding Direction and epidewarp.fsl
actually, I have no idea:). This is a wrapper around the FSL programs. I wrote the code always assuming that the phase encode direction was the row direction. Usually, it gets unpacked that way. Is the data getting reoriented along the way? doug On 11/13/2012 11:34 AM, Satrajit Ghosh wrote: hi doug, just to follow up on this. if i had the phase encode direction (we currently store various dicom attributes in a nifti header extension), where would i provide it? cheers, satra On Tue, Nov 13, 2012 at 11:27 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Clark, the phase encode direction is always lost since that information is not represented in the nifti header. epidewarp.fsl always assumes that the phase encode direction is in the row direction. doug On 11/13/2012 07:32 AM, Clark Fisher wrote: Hi everyone, I recently switched the phase encoding direction of the functional sequence I've been using from F H to R L and ran into a problem with epidewarp.fsl (in version 4). The unwarping was still happening along the F H axis in the new images where phase encoding was R L. (Note: I'm working with NHPs in sphinx position, but I'll describe my problem in standard coordinates to keep everything somewhat simpler) Because thought that epidewarp.fsl might be having a difficult time determining the phase encoding direction, I swapped the position of the F H and R L dimensions in my nifti file (going from LIP to IRP) and the dewarping now seems to work. Is there something going wrong in the unpacking such that the phase encoding information is lost? Also, is the phase encoding information stored anywhere in the nifti, so that I can automatically detect and correct cases like this? Thanks for the help, Clark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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. -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] gstro...@ggmail.com, analysis-b...@nmr.mgh.harvard.edu
Hi Azeez, try using mris_fill. cheers Bruce On Tue, 13 Nov 2012, Azeez Adebimpe wrote: Hi Freesurferers or Experts, I have been trying to convert the watershed bem brain surfaces to vol with mri_fill and mri_surf2vol but not succeed. My main aim is to create mask for outer_skull, inner_skull and other from their respective surfaces. Is there any other method to use? Azeez Azeez Adebimpe ___ 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] Phase Encoding Direction and epidewarp.fsl
Thanks Doug, Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps? -Clark ___ 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] Phase Encoding Direction and epidewarp.fsl
I'm a little confused as to why the rows are not the phase encode direction to begin with. What did you use to convert the dicoms to nifti? doug On 11/13/2012 11:59 AM, Clark Fisher wrote: Thanks Doug, Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps? -Clark -- 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: 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] volume conversion problem
Yes, the problem is rawavg.mgz. When was it created? How many runs do you have in this data set? You can also try using your input volume subject/mri/orig/001.mgz (or what ever it is called). If you only have one run, then rawavg.mgz should just be a copy of 001.mgz doug On 11/12/2012 11:54 AM, Gabriel Gonzalez Escamilla wrote: Here yu are: mri_info brain.mgz Volume information for brain.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 11.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = -0., z_r = 0., c_r = 2.1879 : x_a = -0., y_a = 0., z_a = 1., c_a =11.6591 : x_s = -0., y_s = -1., z_s = -0., c_s = -17.2780 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. -0. 0. 130.1879 -0. 0. 1. -116.3409 -0. -1. -0. 110.7220 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 130.1879 0. -0. -1. 110.7220 -0. 1. -0. 116.3409 0. 0. 0. 1. mri_info rawavg.mgz MRIalloc: could not allocate -512234304 frame Cannot allocate memory As I see, the problem comes from the rawavg.mgz, if I do convert the dicoms into mgz, would this solve the problem, right? or there's anything else I can do? Regards, Gabriel El 12/11/12, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: Can you send the result of mri_info brain.mgz mri_info rawavg.mgz doug On 11/12/2012 10:27 AM, Gabriel Gonzalez Escamilla wrote: Dear FS experts, I'm trying to convert one skull-stripped image from the FS segmentation to a nifti in native space, but I'm having some troubles with it. I'm doing everything with the a to d steps a) cd /root/trabajo/freesurfer/subjects/s00x/mri/ b) mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader c) mri_mask -T 2 rawavg.mgz brain2raw.mgz brainraw.mgz d) mri_convert -odt float brainraw.mgz brain.nii but in step b always get the following error: mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader movvol brain.mgz targvol rawavg.mgz outvol brain2raw.mgz invert 0 tal0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1352942991 MRIalloc: could not allocate -512234304 frame Cannot allocate memory Any ideas how to solve this? Should I to re-run any recon? Many thanks in advanced, Gabriel ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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. -- 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: 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
Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl
I'm using a script that calls unpacksdcmdir. Maybe there is some setting in our config file that forces the orientation? Nothing obvious though. On Nov 13, 2012, at 12:03 PM, Douglas N Greve wrote: I'm a little confused as to why the rows are not the phase encode direction to begin with. What did you use to convert the dicoms to nifti? doug On 11/13/2012 11:59 AM, Clark Fisher wrote: Thanks Doug, Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps? -Clark -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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] Phase Encoding Direction and epidewarp.fsl
Hi Clark, hi Doug fugue has an option that might help here. Here is the relevant excerpt rom calling fugue on the command line (as in fugue of fsl 5.0.1 but I am sure this was also present in fsl 4.1.n): --unwarpdirspecifies direction of warping [x/y/z/x-/y-/z-] (default y) it seems that this might help if set correctly; Clark maybe you can hack epidewarp.fsl to include an export option to supply this information to the script? best Sebastian On Nov 13, 2012, at 09:51 , Clark Fisher wrote: I'm using a script that calls unpacksdcmdir. Maybe there is some setting in our config file that forces the orientation? Nothing obvious though. On Nov 13, 2012, at 12:03 PM, Douglas N Greve wrote: I'm a little confused as to why the rows are not the phase encode direction to begin with. What did you use to convert the dicoms to nifti? doug On 11/13/2012 11:59 AM, Clark Fisher wrote: Thanks Doug, Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps? -Clark -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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 -- Sebastian Moeller telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807-5242 US CDMA: +1-626-807-5242 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Qdec - longitudinal. File missing
Hello Martin, thanks again for your help. We created the .Qdecrc file in the qdec directory. It still gives the same error. Also we made some changes to the .Qdecrc file, for example we changed the ...long.thickness.. to ...long-thickness..., but the error remaines the same. We performed additionally the same analysis on linux, starting with long_mris_slopes, and we updated there also all the files and scripts, but when we open qdec, the error is the same. Qdec just doesn't see the .Qdecrc file. two systems - mac and linux, same error. Are there some other Qdec files that need to be updated ? besides qdec.bin and qdeclibs.tgz (for mac) Best regards, Alex. Le 10/11/2012 9:17 AM, Martin Reuter a écrit : Hi Alex. Take a look at the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial you need to create a .Qdecrc file in the qdec directory to tell qdec about the filenames with the .long in it: Also QDEC will not know about our new files (e.g. lh.long.thickness-spc...). We can tell it to look for them by creating a qdec/.Qdecrc file in the qdec directory that contains the following lines: MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spcYou can then run qdec and do all kinds of analysis on any of those files and other variables from the qdec table: qdec --table ./qdec/cross.qdec.table.datBest, Martin- Original Message - From: Alex Hanganu al.hang...@yahoo.ca To: Martin Reuter mreu...@nmr.mgh.harvard.edu Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Sent: Friday, November 09, 2012 9:47 PM Subject: Re: [Freesurfer] Qdec - longitudinal. File missing Hello Martin, thanks for your answer, I used the --qcache. The cmd was: long_mris_slopes --qdec qdecfile --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time months --fwhm 10 --qcache fsaverage --sd SUBJECTS_DIR All the bases subjects have the specific files after this cmd: lh.long.thickness-avg[pc1/rate/spc].fwhm0[5, 10, 15, 20, 25].fsaverage.mgh but the file that qdec asks for - is missing in all the bases subjects. Qdec asks for: lh.thickness ... but long_mris_slopes created: lh.long.thickness... it seems to be a qdec error ? maybe. btw, i changed the qdec.bin and qdeclibs.tgz with the last versions, from the release notes link. Also i used the last version of long_mris_slopes, from 2012/05/30. We work on mac leopard, but the recon-all -all / -base and -long was performed on linux (cluster). Sincerely, Alex. Le 09/11/2012 9:14 PM, Martin Reuter a écrit : Hi Alex, check the bases of other subjects. Are there any fwhmfsaverage files? Did you run with the --qcache flag? Then these should have been created. Maybe you passed a specific fwhm value different from 10? Best, Martin On Fri, 2012-11-09 at 17:13 -0500, Alex Hanganu wrote: Dear FreeSurfer Experts, we performed the long_mris_slopes cmd and finished without error. According to the Longitudinal Processing Tutorial, we created after that the cross sectional form of the qdec table, and then the qdec/.Qdecrc file. When running the qdec analyses, we receive an error: Couldn't open ...subjects-base/surf/lh.thickness.fwhm.10.fsaverage.mgz or mgh file. The file is missing, it wasn't created. What did we miss ? Thanks, Sincerely, Alex. ___ 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 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
Re: [Freesurfer] bankssts label
Hi Vincent, sorry, I'm not sure. This is an area that Ron Killiany and Marilyn Albert had found sizable effects in prodromal AD patients, which is why Ron included it in his parcellation, but I'm not sure how they decided the extent and location of it. You could email Rahul Desikan and ask him cheers Bruce On Tue, 13 Nov 2012, Mensen, V.T. wrote: Dear Freesurfers, Does anyone know why sometimes the bankssts (banks of the superior temporal sulcus) is only found in the sulcus, and sometimes occupies a sizeable part of an adjacent gyrus (superior temporal / inferior parietal)? The dark-green area is generally only visible in the inflated view, but every so often it is quite pronounced in the main (pial) view as well. Thanks! Vincent Mensen Utrecht -- De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. -- This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. ___ 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] Phase Encoding Direction and epidewarp.fsl
I guess it is possible that Siemens is doing something funny with the images. I've never used sagittal before. On 11/13/2012 12:51 PM, Clark Fisher wrote: I'm using a script that calls unpacksdcmdir. Maybe there is some setting in our config file that forces the orientation? Nothing obvious though. On Nov 13, 2012, at 12:03 PM, Douglas N Greve wrote: I'm a little confused as to why the rows are not the phase encode direction to begin with. What did you use to convert the dicoms to nifti? doug On 11/13/2012 11:59 AM, Clark Fisher wrote: Thanks Doug, Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps? -Clark -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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. -- 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: 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
Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl
Hi Doug, All other things being equal, if you switch from AP to RL phase encoding in an axial acquisition, then the PE direction will switch from the y-axis to the x-axis in the images. It doesn't really have anything to do with Siemens, since the images are written out in a standard anatomical orientation, not according to which axis was readout and which was phase encode. Hope that helps, -MH Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 11/13/12 3:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I guess it is possible that Siemens is doing something funny with the images. I've never used sagittal before. On 11/13/2012 12:51 PM, Clark Fisher wrote: I'm using a script that calls unpacksdcmdir. Maybe there is some setting in our config file that forces the orientation? Nothing obvious though. On Nov 13, 2012, at 12:03 PM, Douglas N Greve wrote: I'm a little confused as to why the rows are not the phase encode direction to begin with. What did you use to convert the dicoms to nifti? doug On 11/13/2012 11:59 AM, Clark Fisher wrote: Thanks Doug, Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps? -Clark -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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. -- 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: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Subgenual ACC - part of the Desikan rostral ACC?
Hello all - I'm unclear on whether the subgenual ACC gets included in the rostral ACC when running parcellations from the Desikan atlas. From the Desikan paper's description and images, it appears to me that the rACC area curves under the genu of the CC and that the caudal boundary there at the genu marks the rostral edge of the subgenual ACC/BA 25? Clarification would be much appreciated! thanks! - Amanda Amanda Schlesinger, MD Department of Psychiatry University of Minnesota Medical School schle...@umn.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] Subgenual ACC - part of the Desikan rostral ACC?
Rahul? On Tue, 13 Nov 2012, Amanda Schlesinger wrote: Hello all - I'm unclear on whether the subgenual ACC gets included in the rostral ACC when running parcellations from the Desikan atlas. From the Desikan paper's description and images, it appears to me that the rACC area curves under the genu of the CC and that the caudal boundary there at the genu marks the rostral edge of the subgenual ACC/BA 25? Clarification would be much appreciated! thanks! - Amanda Amanda Schlesinger, MD Department of Psychiatry University of Minnesota Medical School schle...@umn.edu ___ 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 - longitudinal. File missing
Hi Martin, Yes, that's it, I wasn't changing the Measure in the Design tab ! Thank you very much for the advice and support ! Sincerely, Alex Le 13/11/2012 3:41 PM, Martin Reuter a écrit : Hi Alex, just tested it with our dev version and it works for me. When you setup the subjectsdir and have the file in $SUBJECT_DIR/qdec/.Qdecrc then after starting qdec you should be able to select e.g. long.thickness-rate under 'Measure' in the 'Design' tab. Best, Martin On Tue, 2012-11-13 at 13:51 -0500, Alex Hanganu wrote: Hello Martin, thanks again for your help. We created the .Qdecrc file in the qdec directory. It still gives the same error. Also we made some changes to the .Qdecrc file, for example we changed the ...long.thickness.. to ...long-thickness..., but the error remaines the same. We performed additionally the same analysis on linux, starting with long_mris_slopes, and we updated there also all the files and scripts, but when we open qdec, the error is the same. Qdec just doesn't see the .Qdecrc file. two systems - mac and linux, same error. Are there some other Qdec files that need to be updated ? besides qdec.bin and qdeclibs.tgz (for mac) Best regards, Alex. Le 10/11/2012 9:17 AM, Martin Reuter a écrit : Hi Alex. Take a look at the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial you need to create a .Qdecrc file in the qdec directory to tell qdec about the filenames with the .long in it: Also QDEC will not know about our new files (e.g. lh.long.thickness-spc...). We can tell it to look for them by creating a qdec/.Qdecrc file in the qdec directory that contains the following lines: MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spcYou can then run qdec and do all kinds of analysis on any of those files and other variables from the qdec table: qdec --table ./qdec/cross.qdec.table.datBest, Martin- Original Message - From: Alex Hanganu al.hang...@yahoo.ca To: Martin Reuter mreu...@nmr.mgh.harvard.edu Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Sent: Friday, November 09, 2012 9:47 PM Subject: Re: [Freesurfer] Qdec - longitudinal. File missing Hello Martin, thanks for your answer, I used the --qcache. The cmd was: long_mris_slopes --qdec qdecfile --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time months --fwhm 10 --qcache fsaverage --sd SUBJECTS_DIR All the bases subjects have the specific files after this cmd: lh.long.thickness-avg[pc1/rate/spc].fwhm0[5, 10, 15, 20, 25].fsaverage.mgh but the file that qdec asks for - is missing in all the bases subjects. Qdec asks for: lh.thickness ... but long_mris_slopes created: lh.long.thickness... it seems to be a qdec error ? maybe. btw, i changed the qdec.bin and qdeclibs.tgz with the last versions, from the release notes link. Also i used the last version of long_mris_slopes, from 2012/05/30. We work on mac leopard, but the recon-all -all / -base and -long was performed on linux (cluster). Sincerely, Alex. Le 09/11/2012 9:14 PM, Martin Reuter a écrit : Hi Alex, check the bases of other subjects. Are there any fwhmfsaverage files? Did you run with the --qcache flag? Then these should have been created. Maybe you passed a specific fwhm value different from 10? Best, Martin On Fri, 2012-11-09 at 17:13 -0500, Alex Hanganu wrote: Dear FreeSurfer Experts, we performed the long_mris_slopes cmd and finished without error. According to the Longitudinal Processing Tutorial, we created after that the cross sectional form of the qdec table, and then the qdec/.Qdecrc file. When running the qdec analyses, we receive an error: Couldn't open ...subjects-base/surf/lh.thickness.fwhm.10.fsaverage.mgz or mgh file. The file is missing, it wasn't created. What did we miss ? Thanks, Sincerely, Alex. ___ 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 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 ___ Freesurfer
Re: [Freesurfer] bad acquisition and noise problem.
I'm not engaged in obtaining images, so I don't have any details about the images. I wonder the method which you commented can be applied to images I already earned. If it's not, is there any way to recover SNR after image scanning? Thanks, Youngmin Huh. 2012/11/13 Bruce Fischl fis...@nmr.mgh.harvard.edu what is the bandwidth? The typical way to fix it is to increase the bandwidth. You can probably recover some of the SNR you will lose by reducing your flip angle, which is pretty far from the Ernst angle. Also, minimize your TE (if 4ms is not already the min) cheers Bruce On Tue, 13 Nov 2012, youngmin huh wrote: Hi, 3D SPGR sequences were used. (TR=22, TE=4, thickness=1.4, FOV=240*240, FA=40) If the artifacts are due to B0 distortion, I wonder how I can fix it. Thanks, Youngmin Huh 2012/11/12 Bruce Fischl fis...@nmr.mgh.harvard.edu Can you give us the acquisition details? I suspect this is not noise, but rather B0 distortion. what is the acquisition? And what bandwidth? On Nov 8, 2012, at 2:53 AM, youngmin huh ymin1...@gmail.com wrote: Dear all, I'm working with some images, and they have so much noises on temporal areas. I just ran recon2, but not sure if they'll be segmented properly. Does anyone have a recommendation for dealing with it? I wonder if there is any flag or option for this occasion. I would appreciate any comments or help. I attached an example. Thanks, Youngmin Huh temporal_001.jpg 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/**compliancelinehttp://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] bad acquisition and noise problem.
it's not a question of SNR, the problem appears to me to be that the B0 distortions are so bad that a bunch of the temporal lobe is piled up on top of itself. There's no way to fix that posthoc. If you upload the full volume I'm happy to take a look On Wed, 14 Nov 2012, youngmin huh wrote: I'm not engaged in obtaining images, so I don't have any details about the images.I wonder the method which you commented can be applied to images I already earned. If it's not, is there any way to recover SNR after image scanning? Thanks, Youngmin Huh. 2012/11/13 Bruce Fischl fis...@nmr.mgh.harvard.edu what is the bandwidth? The typical way to fix it is to increase the bandwidth. You can probably recover some of the SNR you will lose by reducing your flip angle, which is pretty far from the Ernst angle. Also, minimize your TE (if 4ms is not already the min) cheers Bruce On Tue, 13 Nov 2012, youngmin huh wrote: Hi, 3D SPGR sequences were used. (TR=22, TE=4, thickness=1.4, FOV=240*240, FA=40) If the artifacts are due to B0 distortion, I wonder how I can fix it. Thanks, Youngmin Huh 2012/11/12 Bruce Fischl fis...@nmr.mgh.harvard.edu Can you give us the acquisition details? I suspect this is not noise, but rather B0 distortion. what is the acquisition? And what bandwidth? On Nov 8, 2012, at 2:53 AM, youngmin huh ymin1...@gmail.com wrote: Dear all, I'm working with some images, and they have so much noises on temporal areas. I just ran recon2, but not sure if they'll be segmented properly. Does anyone have a recommendation for dealing with it? I wonder if there is any flag or option for this occasion. I would appreciate any comments or help. I attached an example. Thanks, Youngmin Huh temporal_001.jpg 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.
[Freesurfer] Fwd: bad acquisition and noise problem.
-- Forwarded message -- From: youngmin huh ymin1...@gmail.com Date: 2012/11/14 Subject: Re: bad acquisition and noise problem. To: Bruce Fischl fis...@nmr.mgh.harvard.edu Thanks for your comment. I would appreciate if you could take a look. Do you want a whole folder of the subjects, or just 001.mgz and log file? Thanks, Youngmin. 2012/11/14 Bruce Fischl fis...@nmr.mgh.harvard.edu it's not a question of SNR, the problem appears to me to be that the B0 distortions are so bad that a bunch of the temporal lobe is piled up on top of itself. There's no way to fix that posthoc. If you upload the full volume I'm happy to take a look On Wed, 14 Nov 2012, youngmin huh wrote: I'm not engaged in obtaining images, so I don't have any details about the images.I wonder the method which you commented can be applied to images I already earned. If it's not, is there any way to recover SNR after image scanning? Thanks, Youngmin Huh. 2012/11/13 Bruce Fischl fis...@nmr.mgh.harvard.edu what is the bandwidth? The typical way to fix it is to increase the bandwidth. You can probably recover some of the SNR you will lose by reducing your flip angle, which is pretty far from the Ernst angle. Also, minimize your TE (if 4ms is not already the min) cheers Bruce On Tue, 13 Nov 2012, youngmin huh wrote: Hi, 3D SPGR sequences were used. (TR=22, TE=4, thickness=1.4, FOV=240*240, FA=40) If the artifacts are due to B0 distortion, I wonder how I can fix it. Thanks, Youngmin Huh 2012/11/12 Bruce Fischl fis...@nmr.mgh.harvard.edu Can you give us the acquisition details? I suspect this is not noise, but rather B0 distortion. what is the acquisition? And what bandwidth? On Nov 8, 2012, at 2:53 AM, youngmin huh ymin1...@gmail.com wrote: Dear all, I'm working with some images, and they have so much noises on temporal areas. I just ran recon2, but not sure if they'll be segmented properly. Does anyone have a recommendation for dealing with it? I wonder if there is any flag or option for this occasion. I would appreciate any comments or help. I attached an example. Thanks, Youngmin Huh temporal_001.jpg 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/**compliancelinehttp://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] aparc+aseg voxels labeled as unknown
What is the aseg label for them? On Nov 13, 2012, at 4:30 PM, Nikhil Chandra nsc2...@columbia.edu wrote: Hello, After completing the FreeSurfer Recommended Reconstruction, we have noticed that in aparc+aseg, many subjects exhibit small clusters of voxels in the medial temporal lobe that are labeled as ctx-lh-unknown or ctx-rh-unknown. These clusters are mostly found on the boundaries between the amygdala, hippocampus, inferior lateral ventricles, and cerebral white matter. Please refer to the attached screen shot for an example. How can we deal with this problem? One possible solution that we thought of was to apply the corresponding label in aseg.mgz for each affected voxel in aparc+aseg.mgz, but we thought we would ask if there is a better way. Thank you, Nikhil Chandra aparc_aseg_unknown_label.jpg ___ 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.
