Re: [Freesurfer] average values per cluster
On 2/8/15 1:48 PM, maaike rive wrote: But how can i run the appropriate preprocessing and smoothing? The --X flag s not recognised using mris_preproc. mri_preproc only uses the fsgd file to get the list of subjects to assure that they are ordered in the same way as when mri_glmfit builds the X matrix. I used the same matrix as X in an FSGD file to do this now, it seems to work, but I do not no if it is correct. Furthermore, If I try to run mri_glmfit --sim for the lGI data, I get an error because fwmh66 is not available. I did not smooth the lGI data and with the DODS/DOSS FSGD models there was no problem, so does this mean my new models are not correct? Wow, it is 66 without smoothing? I'm not sure what to tell you. The lGI is often very smooth, but that seems excessive. You can look for outliers by loading the y files as a time coures in tksurfer (-t flag). If it says at 66 then I don't think you can do the voxel-wise analysis. Was it that way when you used the FSGD file? It could be that your design matrix does not remove the mean offset, so check that too. From: r_maa...@hotmail.com Date: Fri, 6 Feb 2015 21:41:53 +0100 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average values per cluster Ok, thanks! Maaike Op 6 feb. 2015 om 17:49 heeft Douglas N Greve gr...@nmr.mgh.harvard.edu het volgende geschreven: There is not a way to build more flexible models in the FSGD structure. However, you can create your own design matrix and include anything you want in it and pass it to mri_glmfit with --X instead of --fsgd. doug On 02/05/2015 06:13 AM, maaike rive wrote: Hi Doug, I hope I'm not driving you crazy, but I have some additional questions regardig the DOSS/DODS models. Also because of the SPSS discrepancies. First, the model I discussed with you I used to assess diagn x age interactions, regressing out the effects of state and gender. However, in this model all interaction terms are incorporated. Is there a way to build the model only incorporating main effects of diagn, state, gender, age and diagn*age and diagn*state interactions? Since I do not expect any higher order interactions or state* age interactions, for instance (this is biologically not very plausible, although I did not formally test it). Second, for areas where there is no diagn*age interaction I want to use a model without any interaction term with age, so I was thinking to use DOSS (I still want to regress out the effects of age, so it was added as a regressor): diagn1*state1*gender1 diagn1*state1*gender2 diagn1*state2*gender1 diagn1*state2*gender2 diagn2*state1*gender1 diagn2*state1*gender2 diagn2*state2*gender1 diagn2*state2*gender2 age However, here there are still interaction terms with gender in the model. I do want to regress out the effects of gender (since I expect this to be a confounder), without incorporating the interaction term. How should I do this? The only solution I can think of is building a model with gender as additional regressor (containing 0 en 1) and using DOSS. So: diagn1*state1 diagn1*state2 diagn2*state1 diagn2*state2 age gender Does this make sense? Third, if so, it implies that for areas where there is no diagn*state interaction, and where I want to test diagn1 vs diagn2 (regressing out the effects of state, since I expect this to be a confounder), I should again build a new model: diagn1 diagn2 age gender state I realize this is a lot of work, hence I hope you could give me any advice about this. Thanks, Maaike From: r_maa...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 3 Feb 2015 13:18:55 +0100 Subject: Re: [Freesurfer] average values per cluster Hi Doug, Sorry, the statistician doesn't understand it yet; we're currently building freesurfer and SPSS models step by step to find out what's going on, but it's a litte time consuming... so, to be continued! Maaike From: r_maa...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Fri, 30 Jan 2015 20:55:27 +0100 Subject: Re: [Freesurfer] average values per cluster On second thought, I think the reason for the discrepancy is that I included state as a factor instead of covariate in the SPSS model. I ran the model again after having adjusted this and included every possible interaction; now I reach a p value of 0.009 (which is still different but at least significant). But I'll check again Monday! From: r_maa...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Fri, 30 Jan 2015 20:15:07 +0100 Subject: Re: [Freesurfer] average
Re: [Freesurfer] Reduction of image size
Good morning, Bruce. Sounds good. Thank you very much. Regards, Sourav From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, February 09, 2015 8:00 AM To: Freesurfer support list Subject: Re: [Freesurfer] Reduction of image size Hi Sourav that won't work - particularly if you are trying to crop in the a/s dimension. Many brains might squeeze into 160 l/r but probably not all, and certainly not with skull. And there won't be any consistent starting coord as it will depend on where the head is in the FOV. The only way for it to definitely work would be to downsample one dimension to 256/160=1.6mm. If you skull strip you could get away with something higher res. Or use fewer than 70 images. cheers Bruce On Mon, 9 Feb 2015, SOURAV RANJAN KOLE wrote: Hello Bruce, Definitely, I am constructing atlases with these images. Based on the number of available and functioning GPUs in our cluster, I am seemingly able to construct atlases of ~70 images with each image size being 256x256x160 and not of image size 256x256x256. Therefore, I am reslicing and I have not done this before. Please guide me to determine the starting coordinates for extraction. Thank you. Regards, Sourav From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, February 08, 2015 6:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] Reduction of image size Hi Sourav Can you explain why you are reslicing? Cheers Bruce On Feb 8, 2015, at 7:26 PM, SOURAV RANJAN KOLE sourav.k...@utah.edu wrote: Thank you, again, Bruce. How do I determine the starting coordinates for extraction, so I do not cutoff relevant info? Regards, Sourav From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, February 08, 2015 5:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Reduction of image size Hi Sourav mri_extract usage: mri_extract src_dir x0 y0 z0 dx dy dz dst_dir (x0, y0, z0) is the starting coordinate of the rectangle to extract *not* the size. (dx, dy, dz) is the size. Yours should be something like: mri_extract input.mgz 0 0 0 256 256 160 output.mgz or maybe you don't want to start at 0, but further into the volume. Also, definitely do NOT use .img at any point as you will lose direction cosine info cheers Bruce On Sun, 8 Feb 2015, SOURAV RANJAN KOLE wrote: Hello Bruce, Thank you for the prompt reply. Although, mri_extract is creating new files but it is giving me the following error- MRIextractInto: bad src location (256, 256, 160). Also, ITK-SNAP cannot read the new image file. Here is what I am doing: 1. Converting from .mgz to .img mri_convert brainmask.mgz brainmask.img --conform --out_data_type float 2. Reducing size of image mri_extract brainmask.img 256 256 160 1 1 1 new_brainmask.img I would like the new images to be 256x256x160 and voxel size to be 1x1x1. Am I not using mri_extract correctly? Thank you. Regards, Sourav From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, February 08, 2015 4:12 PM To: Freesurfer support list Subject: Re: [Freesurfer] Reduction of image size mri_extract should do the trick Bruce On Sun, 8 Feb 2015, SOURAV RANJAN KOLE wrote: Dear Freesurfer community, Please let me know of an elegant way to reduce image size from 256x256x256 to 256x256x160 and keeping the voxel size the same. The images are currently in analyze format but I have access to mri_convert and ImageConvert. Thank you. Sourav ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail
[Freesurfer] time series data from FSFAST
Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. Cheers, Sabin Khadka___ 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] time series data from FSFAST
Thanks Doug. I am now able to get average time series from cortical ROIs. I usedmri_segstats --annot fsaverage lh aparc --i sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txtHow would I get time series of the sub-cortical ROIs (fmcpr.up.sm5.mni305.2mm.nii.gz)?I tried doingmri_segstats --seg fsaverage/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txtbut it gave me dimension mismatch error. I'd appreciate if you'd direct me on how to get average time series values from subcortical regions. Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, February 9, 2015 1:24 PM Subject: Re: [Freesurfer] time series data from FSFAST Yes, mri_segstats. Run it with --help. See esp example 6 On 2/9/15 12:31 PM, sabin khadka wrote: Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. Cheers, Sabin Khadka ___ 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. ___ 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] Interhemispheric registration of .mgh files
Hi all, We're having some trouble using interhemispheric registration. It works fine for files that are automatically registered eg thickness, volume etc. but not for mgh files, like ?h.w-g.pct.mgh. Is there a way of adding files to xhemi/surf/ so that other surfaces files can be compared between hemispheres? Thanks, Konrad ___ 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] topology defect in freesurfer
Hi Lilla, I would be interested in any tips on processing neonate scans as well. Currently we are wanting to process subjects of 1 month up until 2 years of age through Freesurfer. Help is very much appreciated. Kind regards, Fraukje Coopmans PhD Student | Department Psychiatry | Brain Division | University Medical Center Utrecht Room B01.113 | M +31 646 28 04 00 | E f.m.t.coopm...@umcutrecht.nl On 06 Feb 2015, at 19:03, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Shaheen, Freesurfer does not handle that age-range so it is not applicable for neonates. Send me an email and I will tell you what we are developing now that might be appropriate for you. Lilla On Fri, 6 Feb 2015, Shaheen Ahmed wrote: Hello, I am using freesurfer for neonates but get error at the topology construction (excessive topological defect encountered, could not allocate edges for retesselation). My question is 1) is the freesurfer applicable for neonates? I have tried it for 2 year to 9 year old kid it worked fine. 2) I tried the -old fixer flag and tried to run the recon -all but i get the same error. Any suggestions are appreciated. Thanks, Shaheen _ UT Southwestern Medical Center The future of medicine, today. ___ 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. -- 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] time series data from FSFAST
Yes, mri_segstats. Run it with --help. See esp example 6 On 2/9/15 12:31 PM, sabin khadka wrote: Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. Cheers, Sabin Khadka ___ 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.
[Freesurfer] mri_nu_correct.mni and mri_convert with odd matrix dimensions and -cm flag
Dear FreeSurfer experts, when I run e.g.: mri_nu_correct.mni --i orig.mgz --mask brainmask.mgz --o nu.mgz --n 1 --proto-iters 1000 --uchar transforms/talairach.xfm —cm where orig.mgz and brainmask.mgz have 577 x 577 x 577 voxels, there is an error: $Id: mri_segstats.c,v 1.109 2014/10/17 19:31:46 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.15003/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.15003/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15003/input.mean.dat sysname Linux hostname shuki machine x86_64 user nzaretsk UseRobust 0 Loading ./tmp.mri_nu_correct.mni.15003/ones.mgz Loading orig.mgz ERROR: dimension mismatch between input volume and seg input 577 577 577 seg 578 578 578 I have checkt and it appears that mri_convert orig.mgz orig_out.mgz -cm results in orig_out.mgz having one voxel more, e.g. 578 x 578 x 578, instead of 577 x 577 x 577 This does not happen when one omits the “-cm flag, or when the input volume is 578 x 578 x 578. Is this a bug, or do the image dimensions have to be even for some reason? Thanks! Natalia ___ 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] Probabilistic Tractography
Hello Freesurfer World, I am trying to decide how to threshold my probabilistic tractography data. Does anyone have recommendation on best define a threshold? Thank you, Kate Damme ___ 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] Rerun Tracula adding CVS registration
Hey Anastasia (and list), I decided to go with affine registration to MNI when I processed my longitudinal dataset with Tracula, because I didn't realize that one has the option to do both MNI and CVS registration in parallel. Is there a way to rerun Tracula with the CVS option without having to rerun also with the MNI option? Thanks, Janosch ___ 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] time series data from FSFAST
On 2/9/15 3:16 PM, sabin khadka wrote: Thanks Doug. I am now able to get average time series from cortical ROIs. I used mri_segstats --annot fsaverage lh aparc --i sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txt That's right, but I would use the unsmoothed data since smoothing will cause activity to spill-over between regions. How would I get time series of the sub-cortical ROIs (fmcpr.up.sm5.mni305.2mm.nii.gz)? I tried doing mri_segstats --seg fsaverage/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txt but it gave me dimension mismatch error. I'd appreciate if you'd direct me on how to get average time series values from subcortical regions. Use fsaverage/mri.2mm/aseg.mgz doug Cheers, Sabin Khadka *From:* Douglas Greve gr...@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, February 9, 2015 1:24 PM *Subject:* Re: [Freesurfer] time series data from FSFAST Yes, mri_segstats. Run it with --help. See esp example 6 On 2/9/15 12:31 PM, sabin khadka wrote: Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. Cheers, Sabin Khadka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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] time series data from FSFAST
Hi Doug- Works fine. I appreciate your help. Related but different question: Would you help me understand how the QA value(0-1)while checking registration using following command is calculated. tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, February 9, 2015 3:32 PM Subject: Re: [Freesurfer] time series data from FSFAST On 2/9/15 3:16 PM, sabin khadka wrote: Thanks Doug. I am now able to get average time series from cortical ROIs. I used mri_segstats --annot fsaverage lh aparc --i sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txt That's right, but I would use the unsmoothed data since smoothing will cause activity to spill-over between regions. How would I get time series of the sub-cortical ROIs (fmcpr.up.sm5.mni305.2mm.nii.gz)? I tried doing mri_segstats --seg fsaverage/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txt but it gave me dimension mismatch error. I'd appreciate if you'd direct me on how to get average time series values from subcortical regions. Use fsaverage/mri.2mm/aseg.mgz doug Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, February 9, 2015 1:24 PM Subject: Re: [Freesurfer] time series data from FSFAST Yes, mri_segstats. Run it with --help. See esp example 6 On 2/9/15 12:31 PM, sabin khadka wrote: Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. Cheers, Sabin Khadka ___ 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. ___ 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. ___ 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 couldn't receive input from keyboard, ubuntu 14.04
Dear FreeSurfer Expert, I've run qdec to do group analysis and got display of result. However, while I tried to change the threshold, I found I can't change or input anything...Then, I also found that I cannot change the Common-Space Subject...Is there approach to address this issue? Best, Zhichao -- *Zhichao Xia* National Key Laboratory of Cognitive Neuroscience and Learning IDG/McGovern Institute for Brain Research, Beijing Normal University Center for Collaboration and Innovation in Brain and Learning Sciences, Beijing Normal University Division of Child and Adolescent Psychiatry, Department of Psychiatry, UCSF Mobile: +1 (415) 712-3749; +86 13720002046 E-mail: xiazc_...@163.comxiazc_...@163.com; xiazc@gmail.com; zhichao@ucsf.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] Rerun Tracula adding CVS registration
Hi Janosch - Yes, it's possible. In your config file use: set doregmni = 0 set doregcvs = 1 You do not need to rerun any of the preprocessing steps before the inter-subject registration, so skip those when you run trac-all -prep to save time. Hope this helps, a.y On Mon, 9 Feb 2015, Janosch Linkersdörfer wrote: Hey Anastasia (and list), I decided to go with affine registration to MNI when I processed my longitudinal dataset with Tracula, because I didn't realize that one has the option to do both MNI and CVS registration in parallel. Is there a way to rerun Tracula with the CVS option without having to rerun also with the MNI option? Thanks, Janosch ___ 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] Rerun Tracula adding CVS registration
Great, thanks! Am 09.02.2015 um 13:10 schrieb Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Janosch - Yes, it's possible. In your config file use: set doregmni = 0 set doregcvs = 1 You do not need to rerun any of the preprocessing steps before the inter-subject registration, so skip those when you run trac-all -prep to save time. Hope this helps, a.y On Mon, 9 Feb 2015, Janosch Linkersdörfer wrote: Hey Anastasia (and list), I decided to go with affine registration to MNI when I processed my longitudinal dataset with Tracula, because I didn't realize that one has the option to do both MNI and CVS registration in parallel. Is there a way to rerun Tracula with the CVS option without having to rerun also with the MNI option? Thanks, Janosch The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA FA _Avg_Weight vs FA_Avg_Center differences and interpretation
Hi Alexander - When you average over a larger region, you are potentially reducing noise but you may also potentially wash out an effect that is very localized by including more voxels where the effect is not present. That's the difference between the two measures, so they are at different points along the false positive/false negative trade-off. One other option would be to examine if your effect is localized by looking at the FA along the tract (from the pathstats.byvoxel.txt files) instead of averaging over the whole tract. Hope this helps, a.y On Mon, 9 Feb 2015, Alexander Tomyshev wrote: Dear Anastasia and Freesurfer team, I used TRACULA to get FA values for two groups: patients and controls. After that, I ran between group comparison and got circa 0.05 p-values for FA _Avg_Weight values BUT circa 0.001-0.005 p-values for FA_Avg_Center for the same tract. Then I ran correlation analysis and found out that some clinical scores of patients correlate with FA_Avg_Weight values (p-value of c. 0.02) and with FA _Avg_Center values (but with p-values of c. 0.002). So the correlation with FA _Avg_Center is more significant than correlation with FA_Avg_Weight. Once again, when I use FA_Avg_Weight in between-group comparison I got non-significant results (slightly 0.05 p-value), but when I use FA_Avg_Center in such comparison I got significant group difference (c. 0.001-0.005 p-values). My question is – can I use these results and say that there is a statistically significant difference in FA values in some tracts? Of course, I will mention that these difference is significant when we compare average FA values of the highest-probability path only and does not reach statistical significance if we compare average values over the entire tract weighted by the value of the probability distribution at every tract’s voxel. As I understand, theoretically and logically, comparison of average FA values of the highest-probability path only (instead of comparing FA_Avg_Weight values) has more statistical power to detect more subtle differences between groups. And in my case comparison of FA_Avg_Weight values just has not enough statistical power to detect such subtle difference. Am I right? I will very appreciate and will be happy to hear any of your thoughts concerning written above and especially any thoughts on how to interpret such difference between results using FA _Avg_Weight and FA_Avg_Center values. Thank you in advance. Kind regards, Alexander Tomyshev Laboratory of Neuroimaging and Multimodal Analysis, Mental Health Research Center of the Russian Academy of Medical Sciences, 34 Kashirskoe shosse, 115522 Moscow, Russia Email.: alexander.tomys...@gmail.com ___ 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] time series data from FSFAST
That is the cost of the registration. You can look in Greve Fischl 2009 to see how it is computed. doug On 2/9/15 3:45 PM, sabin khadka wrote: Hi Doug- Works fine. I appreciate your help. Related but different question: Would you help me understand how the QA value(0-1)while checking registration using following command is calculated. tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum Cheers, Sabin Khadka *From:* Douglas Greve gr...@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, February 9, 2015 3:32 PM *Subject:* Re: [Freesurfer] time series data from FSFAST On 2/9/15 3:16 PM, sabin khadka wrote: Thanks Doug. I am now able to get average time series from cortical ROIs. I used mri_segstats --annot fsaverage lh aparc --i sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txt That's right, but I would use the unsmoothed data since smoothing will cause activity to spill-over between regions. How would I get time series of the sub-cortical ROIs (fmcpr.up.sm5.mni305.2mm.nii.gz)? I tried doing mri_segstats --seg fsaverage/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txt but it gave me dimension mismatch error. I'd appreciate if you'd direct me on how to get average time series values from subcortical regions. Use fsaverage/mri.2mm/aseg.mgz doug Cheers, Sabin Khadka *From:* Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, February 9, 2015 1:24 PM *Subject:* Re: [Freesurfer] time series data from FSFAST Yes, mri_segstats. Run it with --help. See esp example 6 On 2/9/15 12:31 PM, sabin khadka wrote: Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. Cheers, Sabin Khadka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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.
[Freesurfer] Error in recon-all
Hi Freesurfer support, I am receiving an error from recon-all and would be happy to get your opinion. This dataset, I am processing, is generated by a 3D MPR (Sagittal orientation) protocol. It’s only one of many datasets I have and this is the only one giving me problems… The run seems to generate the typical directory listing: total 0 drwxrwxr-x 12 noambe staff 408 Feb 8 19:24 . drwxr-xr-x@ 20 noambe staff 680 Feb 9 07:49 .. drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 bem drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 label drwxrwxr-x 10 noambe staff 340 Feb 8 19:28 mri drwxrwxr-x 10 noambe staff 340 Feb 8 19:28 scripts drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 src drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 stats drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 surf drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 tmp drwxrwxr-x 4 noambe staff 136 Feb 8 19:27 touch drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 trash but the ‘mri’ folder, for example, is missing most of the data noambe-mac:03_FSseg noambe$ cd mri noambe-mac:mri noambe$ l total 50112 drwxrwxr-x 10 noambe staff 340 Feb 8 19:28 . drwxrwxr-x 12 noambe staff 408 Feb 8 19:24 .. -rw-rw-r-- 1 noambe staff 21230 Feb 8 19:28 mri_nu_correct.mni.log -rw-rw-r-- 1 noambe staff 21230 Feb 8 19:26 mri_nu_correct.mni.log.bak drwxrwxr-x 3 noambe staff 102 Feb 8 19:25 orig -rw-rw-r-- 1 noambe staff 6915766 Feb 8 19:25 orig.mgz -rw-rw-r-- 1 noambe staff 21230 Feb 8 19:28 orig_nu.log -rw-rw-r-- 1 noambe staff 6175023 Feb 8 19:28 orig_nu.mgz -rw-rw-r-- 1 noambe staff 12484984 Feb 8 19:25 rawavg.mgz drwxrwxr-x 8 noambe staff 272 Feb 8 19:28 transforms noambe-mac:mri noambe$ The whole thing runs for a few minutes before it exists with errors. I’m attaching the output of the recon-all run. Thanks in advance, — Noam -- Noam Ben-Eliezer, PhD Adjunct Assistant Professor of Radiology Center for Biomedical-Imaging New-York University Medical School noam.ben-elie...@nyumc.orgmailto:noam.ben-elie...@nyumc.org Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/noambe/Desktop/NYU_dynamic_sort/MS_project/Data_MS/03__MRN Actual FREESURFER_HOME /Applications/freesurfer Darwin noambe-mac.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64 /Users/noambe/Desktop/NYU_dynamic_sort/MS_project/Data_MS/03__MRN/03_FSseg \n mri_convert /Users/noambe/Desktop/NYU_dynamic_sort/MS_project/Data_MS/03__MRN/SAG3DMPR/1.3.12.2.1107.5.2.19.45219.2014072409313512608864296.dcm /Users/noambe/Desktop/NYU_dynamic_sort/MS_project/Data_MS/03__MRN/03_FSseg/mri/orig/001.mgz \n mri_convert /Users/noambe/Desktop/NYU_dynamic_sort/MS_project/Data_MS/03__MRN/SAG3DMPR/1.3.12.2.1107.5.2.19.45219.2014072409313512608864296.dcm /Users/noambe/Desktop/NYU_dynamic_sort/MS_project/Data_MS/03__MRN/03_FSseg/mri/orig/001.mgz $Id: mri_convert.c,v 1.206 2013/11/12 03:15:51 greve Exp $ reading from /Users/noambe/Desktop/NYU_dynamic_sort/MS_project/Data_MS/03__MRN/SAG3DMPR/1.3.12.2.1107.5.2.19.45219.2014072409313512608864296.dcm... Getting Series No INFO: Found 194 files in /Users/noambe/Desktop/NYU_dynamic_sort/MS_project/Data_MS/03__MRN/SAG3DMPR INFO: Scanning for Series Number 13 Scanning Directory INFO: found 192 files in series INFO: loading series header info. RunNo = 12 INFO: sorting. INFO: (256 256 192), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix - 1.0 0.0 0.0 0.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0; FileName /Users/noambe/Desktop/NYU_dynamic_sort/MS_project/Data_MS/03__MRN/SAG3DMPR/1.3.12.2.1107.5.2.19.45219.2014072409313470776164148.dcm Identification NumarisVersyngo MR D13C ScannerModel Skyra PatientName ^^ Date and time StudyDate 20140724 StudyTime 090715.984000 SeriesTime093137.62 AcqTime 092716.187500 Acquisition parameters PulseSeq *tfl3d1_16ns Protocol SAG 3D MPR PhEncDir ROW EchoNo1 FlipAngle 8 EchoTime 2.72 InversionTime 900 RepetitionTime2100 PhEncFOV 256 ReadoutFOV256 Image information RunNo 12 SeriesNo 13 ImageNo 192 NImageRows256 NImageCols256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos100.5353 158.1837 110.8325 VolRes 1. 1. 1. VolDim256
Re: [Freesurfer] TRACULA FA _Avg_Weight vs FA_Avg_Center differences and interpretation
Hi Alexander - These measures (both averages and along-the-tract values) are extracted in each subject's native space, so inter-subject registration is not an issue in the difference that you found. I suspect it is because the along-the-tract measures are sampled at a certain number of cross-sections along the tract, so averaging over these cross-sections and averaging over the whole tract is going to be slightly different. a.y On Tue, 10 Feb 2015, Alexander Tomyshev wrote: Anastasia, thank you for the prompt response. It is helpful. I’ve already examined pathstats.byvoxel.txt files combining them with “-stat” command. First, I compared every voxel along the particular tract. Then I split this tract by 3 equal parts and tried to calculate between-group difference at these 3 parts. But in both cases (every single voxel and 3 parts) I got smaller p-values than in case of analyzing the whole highest-probability path (~0.015 vs ~0.004 uncorrected for multiple comparison). So I decided that analysis of the whole path gave me some system effect (“summarized” effect of differences in different voxels along the tract). By the way! I took a file “tract_name.avg33_mni_bbr.FA” and calculated average FA values for the whole path (average of all points along the path) for every 61 subject from my sample. Then I compared these values with FA_Avg_Center values from pathstats.overall.txt. And I got difference (0.622 vs 0.628 for all 61 subjects, p-value 0.59). What is a main cause of such difference? As I understand this deference arises from some subjects tracts’ alignment procedure. Alexander 2015-02-10 1:23 GMT+04:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Alexander - When you average over a larger region, you are potentially reducing noise but you may also potentially wash out an effect that is very localized by including more voxels where the effect is not present. That's the difference between the two measures, so they are at different points along the false positive/false negative trade-off. One other option would be to examine if your effect is localized by looking at the FA along the tract (from the pathstats.byvoxel.txt files) instead of averaging over the whole tract. Hope this helps, a.y On Mon, 9 Feb 2015, Alexander Tomyshev wrote: Dear Anastasia and Freesurfer team, I used TRACULA to get FA values for two groups: patients and controls. After that, I ran between group comparison and got circa 0.05 p-values for FA _Avg_Weight values BUT circa 0.001-0.005 p-values for FA_Avg_Center for the same tract. Then I ran correlation analysis and found out that some clinical scores of patients correlate with FA_Avg_Weight values (p-value of c. 0.02) and with FA _Avg_Center values (but with p-values of c. 0.002). So the correlation with FA _Avg_Center is more significant than correlation with FA_Avg_Weight. Once again, when I use FA_Avg_Weight in between-group comparison I got non-significant results (slightly 0.05 p-value), but when I use FA_Avg_Center in such comparison I got significant group difference (c. 0.001-0.005 p-values). My question is – can I use these results and say that there is a statistically significant difference in FA values in some tracts? Of course, I will mention that these difference is significant when we compare average FA values of the highest-probability path only and does not reach statistical significance if we compare average values over the entire tract weighted by the value of the probability distribution at every tract’s voxel. As I understand, theoretically and logically, comparison of average FA values of the highest-probability path only (instead of comparing FA_Avg_Weight values) has more statistical power to detect more subtle differences between groups. And in my case comparison of FA_Avg_Weight values just has not enough statistical power to detect such subtle difference. Am I right? I will very appreciate and will be happy to hear any of your thoughts concerning written above and especially any thoughts on how to interpret such difference between results using FA _Avg_Weight and FA_Avg_Center values. Thank you in advance. Kind regards, Alexander Tomyshev Laboratory of Neuroimaging and Multimodal
Re: [Freesurfer] Reduction of image size
Hi Sourav that won't work - particularly if you are trying to crop in the a/s dimension. Many brains might squeeze into 160 l/r but probably not all, and certainly not with skull. And there won't be any consistent starting coord as it will depend on where the head is in the FOV. The only way for it to definitely work would be to downsample one dimension to 256/160=1.6mm. If you skull strip you could get away with something higher res. Or use fewer than 70 images. cheers Bruce On Mon, 9 Feb 2015, SOURAV RANJAN KOLE wrote: Hello Bruce, Definitely, I am constructing atlases with these images. Based on the number of available and functioning GPUs in our cluster, I am seemingly able to construct atlases of ~70 images with each image size being 256x256x160 and not of image size 256x256x256. Therefore, I am reslicing and I have not done this before. Please guide me to determine the starting coordinates for extraction. Thank you. Regards, Sourav From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, February 08, 2015 6:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] Reduction of image size Hi Sourav Can you explain why you are reslicing? Cheers Bruce On Feb 8, 2015, at 7:26 PM, SOURAV RANJAN KOLE sourav.k...@utah.edu wrote: Thank you, again, Bruce. How do I determine the starting coordinates for extraction, so I do not cutoff relevant info? Regards, Sourav From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, February 08, 2015 5:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Reduction of image size Hi Sourav mri_extract usage: mri_extract src_dir x0 y0 z0 dx dy dz dst_dir (x0, y0, z0) is the starting coordinate of the rectangle to extract *not* the size. (dx, dy, dz) is the size. Yours should be something like: mri_extract input.mgz 0 0 0 256 256 160 output.mgz or maybe you don't want to start at 0, but further into the volume. Also, definitely do NOT use .img at any point as you will lose direction cosine info cheers Bruce On Sun, 8 Feb 2015, SOURAV RANJAN KOLE wrote: Hello Bruce, Thank you for the prompt reply. Although, mri_extract is creating new files but it is giving me the following error- MRIextractInto: bad src location (256, 256, 160). Also, ITK-SNAP cannot read the new image file. Here is what I am doing: 1. Converting from .mgz to .img mri_convert brainmask.mgz brainmask.img --conform --out_data_type float 2. Reducing size of image mri_extract brainmask.img 256 256 160 1 1 1 new_brainmask.img I would like the new images to be 256x256x160 and voxel size to be 1x1x1. Am I not using mri_extract correctly? Thank you. Regards, Sourav From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, February 08, 2015 4:12 PM To: Freesurfer support list Subject: Re: [Freesurfer] Reduction of image size mri_extract should do the trick Bruce On Sun, 8 Feb 2015, SOURAV RANJAN KOLE wrote: Dear Freesurfer community, Please let me know of an elegant way to reduce image size from 256x256x256 to 256x256x160 and keeping the voxel size the same. The images are currently in analyze format but I have access to mri_convert and ImageConvert. Thank you. Sourav ___ 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
Re: [Freesurfer] Error in recon-all
Hi Noam it looks like the talairach alignment failed. You can usually find answers on our wiki for what to do in this type of case. For example: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_tktools cheers Bruce On Mon, 9 Feb 2015, Ben Eliezer, Noam wrote: Hi Freesurfer support, I am receiving an error from recon-all and would be happy to get your opinion. This dataset, I am processing, is generated by a 3D MPR (Sagittal orientation) protocol. It’s only one of many datasets I have and this is the only one giving me problems… The run seems to generate the typical directory listing: total 0 drwxrwxr-x 12 noambe staff 408 Feb 8 19:24 . drwxr-xr-x@ 20 noambe staff 680 Feb 9 07:49 .. drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 bem drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 label drwxrwxr-x 10 noambe staff 340 Feb 8 19:28 mri drwxrwxr-x 10 noambe staff 340 Feb 8 19:28 scripts drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 src drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 stats drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 surf drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 tmp drwxrwxr-x 4 noambe staff 136 Feb 8 19:27 touch drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 trash but the ‘mri’ folder, for example, is missing most of the data noambe-mac:03_FSseg noambe$ cd mri noambe-mac:mri noambe$ l total 50112 drwxrwxr-x 10 noambe staff 340 Feb 8 19:28 . drwxrwxr-x 12 noambe staff 408 Feb 8 19:24 .. -rw-rw-r-- 1 noambe staff 21230 Feb 8 19:28 mri_nu_correct.mni.log -rw-rw-r-- 1 noambe staff 21230 Feb 8 19:26 mri_nu_correct.mni.log.bak drwxrwxr-x 3 noambe staff 102 Feb 8 19:25 orig -rw-rw-r-- 1 noambe staff 6915766 Feb 8 19:25 orig.mgz -rw-rw-r-- 1 noambe staff 21230 Feb 8 19:28 orig_nu.log -rw-rw-r-- 1 noambe staff 6175023 Feb 8 19:28 orig_nu.mgz -rw-rw-r-- 1 noambe staff 12484984 Feb 8 19:25 rawavg.mgz drwxrwxr-x 8 noambe staff 272 Feb 8 19:28 transforms noambe-mac:mri noambe$ The whole thing runs for a few minutes before it exists with errors. I’m attaching the output of the recon-all run. Thanks in advance, — Noam -- Noam Ben-Eliezer, PhD Adjunct Assistant Professor of Radiology Center for Biomedical-Imaging New-York University Medical School noam.ben-elie...@nyumc.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] TRACULA FA _Avg_Weight vs FA_Avg_Center differences and interpretation
Dear Anastasia and Freesurfer team, I used TRACULA to get FA values for two groups: patients and controls. After that, I ran between group comparison and got circa 0.05 p-values for FA _Avg_Weight values BUT circa 0.001-0.005 p-values for FA_Avg_Center for the same tract. Then I ran correlation analysis and found out that some clinical scores of patients correlate with FA_Avg_Weight values (p-value of c. 0.02) and with FA _Avg_Center values (but with p-values of c. 0.002). So the correlation with FA _Avg_Center is more significant than correlation with FA_Avg_Weight. Once again, when I use FA_Avg_Weight in between-group comparison I got non-significant results (slightly 0.05 p-value), but when I use FA_Avg_Center in such comparison I got significant group difference (c. 0.001-0.005 p-values). My question is – can I use these results and say that there is a statistically significant difference in FA values in some tracts? Of course, I will mention that these difference is significant when we compare average FA values of the highest-probability path only and does not reach statistical significance if we compare average values over the entire tract weighted by the value of the probability distribution at every tract’s voxel. As I understand, theoretically and logically, comparison of average FA values of the highest-probability path only (instead of comparing FA_Avg_Weight values) has more statistical power to detect more subtle differences between groups. And in my case comparison of FA_Avg_Weight values just has not enough statistical power to detect such subtle difference. Am I right? I will very appreciate and will be happy to hear any of your thoughts concerning written above and especially any thoughts on how to interpret such difference between results using FA _Avg_Weight and FA_Avg_Center values. Thank you in advance. Kind regards, Alexander Tomyshev Laboratory of Neuroimaging and Multimodal Analysis, Mental Health Research Center of the Russian Academy of Medical Sciences, 34 Kashirskoe shosse, 115522 Moscow, Russia Email.: alexander.tomys...@gmail.com ___ 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.
