[Freesurfer] Hippocampal sufields in MNI templates
Dear freesurfer users,I was wondering: is there any way to get normalized ROIs for hippocampal subfields in MNI space? Is anything speaking against for example, running freesurfer with subcortical segmentation on an MNI template? cheers and kind regards, Lorenzo Pasquini___ 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] Group differences of functional connectivity differ in SPM and FSL
Dear users, I writhe in the hope somebody encountered a similar problem. I have individual normalized maps of intrinisc brain networks from a dual regression. This maps are projected back into individual subject space and further into individual surface space. Finally I normalize this maps into fslaverage and look at group differences in functional connectivity. I have following problem:the statistical results for the pDMN differ in surface space compared to SPM:While group A has increased functional connectivity compared to group B when i compare the dual regression maps in SPM (this result is in line with literature), group A has decreased functional connectivity compared to group B when i compare the dual regression maps in surface space. Me and the IT expert have checked the script and the test contrast and repeated the analysis several times, we could not find any evident error (example: subject order inverted., matrix code inverted) The steps I perform are the following:1. individual MELODIC to preprocess functional data2. bbregister is used to coregister the preprocessed functional data to anatomy. Functional data is not changed, just the transformation matrix is saved (register.dat). Following warning is found: "initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1" . Is this relevant?3. Dual regression is performed with normalized functional data and maps are statistically evaluated4. Normalized dual regression maps are backprojected into native space by using the inverse normalization matrix derived from the first preprocessing through MELODIC5. vol2surf is used to project native space maps into individual surface space derived from freesurfer (using register.dat file) 6. mris_preproc and mri_glmfit are used to normalize the individual surface activation maps into fslaverage and the two sample ttest is performed. I am really wondering how the results can be inverted just in this SINGLE NETWORK, as they are comparable for other networks. The backprojection into native space is crucial for my research question. Hope is the last to die:)thanks and cheers, Lorenzo ___ 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] normalizing activation maps
Dear Freesurfers, I have a question regarding normalization of functional activation maps. Let us assume I have functional activation maps on a vertex space (e.g. mgh files reflecting degree centrality, which do not need previous normalization of functional data). After resampling activation maps into individual vertex space (bbregister and vol2surf), I want to investigate if any differences across two groups are detectable regarding this activation maps. Which pipeline/command/stream is better to use for first normalize the activation maps into a common template and then create an output that can be implemented into mri_glmfit ? Should fsfast be used? Or is mri_surf2surf better? Thanks a lot, Lorenzo___ 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] mincost bb_register
Dear Freesurfer users, I have used the command bb_register to automatically register raw fMRI data on the anatomy. The output looks visually fine, however the mincost file gives me values around 0.5 for my subjects. Is this range acceptable? Does anybody has a hint on how the registration could be optimized? I use init-fsl and --bold as contrast in my bbregister command. Best, Lorenzo___ 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] Vertex space
Dear Bruce, thank you very much for the quick reply. The aim of our study is to investigate the correspondence of cortical thickness and measures of functional connectivity (e.g. from ICA) on a vertex-based within-subject level. However, we are not sure how to implement this in freesurfer, initially we tried to sample our functional connectivity maps into vertex space without much success. If I understood it correctly, the right strategy would be to to sample the raw fMRI data into vertex space (using nifti format), then perform our functional connectivity analysis on the resampled data, use the inverse normalization matrices to back-reconstruct our functional maps into vertex space, finally investigate the relationship, right? Some practical questions: the output of bbregister and mri_vol2surf is still in nifti format? are this steps building new images or overwrithing the old ones? Can we transform the cortical surface (bearing vertex-based information of cortical thickness) into nifti format? Thank you again for your help! Sincerely, Lorenzo Il Mercoledì 3 Settembre 2014 18:18, Bruce Fischl ha scritto: Hi Lorenzo we need more information if we are going to be able to help you. What is not working? You should be able to use bbregister on the fMRI data to register it to the surface, then mri_vol2surf to sample it onto the vertex mesh. Note that you should avoid .img format! Use nifti instead - analyze doesn't have enough information to reliabily distinguish left from right. cheers Bruce On Wed, 3 Sep 2014, lorenzo pasquini wrote: > Dear Freesurfer users, > > I was wondering if it is possible to transform functional connectivity > images (.img format) derived e.g. from an ICA of resting state fMRI data > into vertex space reflecting cortical thickness (derived from the Freesurfer > pipeline on anatomical data). We have been trying hard with commands as > mrivol2surface and bbregister without much success. Do you have any > suggestions why it is not working? Can a correspondence of activity and > structure be implemented in Freesurfer only if the activation maps are > derived from the freesurfer pipeline? > Any help is welcome! > Cheers, > > Lorenzo > > 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] Vertex space
Dear Freesurfer users, I was wondering if it is possible to transform functional connectivity images (.img format) derived e.g. from an ICA of resting state fMRI data into vertex space reflecting cortical thickness (derived from the Freesurfer pipeline on anatomical data). We have been trying hard with commands as mrivol2surface and bbregister without much success. Do you have any suggestions why it is not working? Can a correspondence of activity and structure be implemented in Freesurfer only if the activation maps are derived from the freesurfer pipeline? Any help is welcome! Cheers, Lorenzo___ 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] Prroblem with segmentation using aparc 2009 labels
Dear Freesurfer users, I used freesurfer to extract the cortical thickness of several regions, which are saved in the aparc.a2009s.stats text file. To create a mask of this regions for further analyzes I used the command line: mri_binarize --i aparc+aseg.mgz --min number --max number -- o testname.mask.nii as numbers I used for example 11126.5 and 11127.5 (ctx_lh_G_parietal_sup) derived from the aparc.a2009.s FreesurferColorLUT table Unfortunately, the created mask is empty and freesurfer "tells" me that there are no voxels in the created nii image. Did anybody experience the same problem? Am I using the wrong binarization command line? Should I download an extra toolbox? How can I solve this problem? Thank you very much and kind regards, Lorenzo Pasquini___ 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] hippocampal segmentation converting mgz to nii
Dear Koen, thank you very much for your help!! by summing the intensities and dividing by 255 I get the same volumes estimated by freesurfer. Thank you again and greets, Lorenzo Pasquini --- Ven 7/12/12, Koen Van Leemput ha scritto: Da: Koen Van Leemput Oggetto: Re: [Freesurfer] hippocampal segmentation converting mgz to nii A: "lorenzo pasquini" Cc: "Freesurfer Mailinglist" Data: Venerdì 7 dicembre 2012, 11:47 Hi Lorenzo, The correct way to calculate the expected (not an integer value) number of voxels belonging to a subfield is by summing ( intensity / 255 ) across all voxels. Not sure where things go wrong: the integer values you report are a bit suspicious, or perhaps some rescaling of image intensities is done during the conversion. You should also be able to convert from .mgz to .nii using the command "kvlConvert" Cheers, Koen On Wed, Nov 28, 2012 at 8:21 AM, lorenzo pasquini wrote: Dear freesurfer users, I have used freesurfer to segment hippocampal subfields. Then I used freeview to convert the derived .mgz files in .nii files for further analysis. I estimated the hippocampal subfields volumes with the command: kvlQuantifyPosteriorProbabilityImages $ FREESURFER_HOME/ data/ GEMS/ compressionLookupTable.txt posterior_right_* posterior_Right-Hippocampus.mgz I have calculated the number of voxels in the converted .nii files using SPM and realized that they do not fit the estimated volumes through freesurfer Example for CA2-2 estimated voxel number though freesurfer: 6851 voxels found in .nii file: 15812 Did somebody had similar problems? Do you have any suggestion? Are there any incompatibilities between SPM and freesurfer? I did not find any apparent error in my counting script. Thank you very much and regards, Lorenzo Pasquini Can. Ph. D., Medical Life Science and Technology (Technische Universität Muenchen) Neuroimaging Lab, Neuroradiology Klinikum r. d. Isar (Technische Universität) 81675 München Tel.: 0049 (0) 89 4140-7666 ___ 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. -Segue allegato- ___ 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] voxel number estimation kvlQuantifyPosteriorProbabilityImages
Dear freesurfer users, I have a question regarding the kvlQuantifyPosteriorProbabilityImages command to quantify hippocampal subfield volumes. Are all voxels with a probability value bigger than 0 counted? Or is the command applying any threshold for the estimation? I have transformed the subfield .mgz images in .nii images. The number of voxels with a probability bigger than 0 in the nii images do not correspond to the estimations extracted with the kvlQuantifyPosteriorProbabilityImages command. Thank you! yours, Lorenzo Pasquini Can. Ph. D., Medical Life Science and Technology (Technische Universität Muenchen) Neuroimaging Lab, Neuroradiology Klinikum r. d. Isar (Technische Universität) 81675 München Tel.: 0049 (0) 89 4140-7666___ 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] hippocampal segmentation converting mgz to nii
Dear freesurfer users, I have used freesurfer to segment hippocampal subfields. Then I used freeview to convert the derived .mgz files in .nii files for further analysis. I estimated the hippocampal subfields volumes with the command: kvlQuantifyPosteriorProbabilityImages $ FREESURFER_HOME/ data/ GEMS/ compressionLookupTable.txt posterior_right_* posterior_Right-Hippocampus.mgz I have calculated the number of voxels in the converted .nii files using SPM and realized that they do not fit the estimated volumes through freesurfer Example for CA2-2 estimated voxel number though freesurfer: 6851 voxels found in .nii file: 15812 Did somebody had similar problems? Do you have any suggestion? Are there any incompatibilities between SPM and freesurfer? I did not find any apparent error in my counting script. Thank you very much and regards, Lorenzo Pasquini Can. Ph. D., Medical Life Science and Technology (Technische Universität Muenchen) Neuroimaging Lab, Neuroradiology Klinikum r. d. Isar (Technische Universität) 81675 München Tel.: 0049 (0) 89 4140-7666 ___ 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] I: hippocampal subfield segmentation
hello carolina to me it took about 5-6 hours. greets, lorenzo Da: Carolina Valencia A: Freesurfer Mailing List Inviato: Giovedì 30 Agosto 2012 20:37 Oggetto: [Freesurfer] hippocampal subfield segmentation Hi Freesurfer community, A quick question, how long takes to run the hippocampal subfield segmentation for a subject that has already run the typical recon-all pipeline? Thank you, -- -- Carolina Valencia M ___ 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] hippocampus subfilelds mask
Dear Freesurfer experts, I successfully run a hippocampal subfield segmentation on anatomical data of one subject (resolution 1 mm^3). Now I am building hippocampal subfields masks. I used the FreeView interface to load the mgz volume files of hippocampal subfields. I saved each subfield separately, binarized and transformed it in my dimension space through marsbar (spm8). I tried as well the mri_binarize command with the codes for hippocampal subfields, but the extracted masks were strangely empty (no voxels found). Is this a right way and the simplest way to build hippocampal subfields ROIs? Is there any apparent error in these procedure? Binarized mask might overlap, is there any suggested threshold? Thank you very much, greets, Lorenzo Pasquini___ 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] Hippocampal segmentation: version needed
Dear Freesurfer experts, I used freesurfer v4.3.0 on anatomical data (T1). I am trying to segment hippocampal subfields with the following command: recon-all -s subjname -hippo-subfields unfortunately I get the following error: ERROR: Flag -hippo-subfields unrecognized I have already the files aseg.mgz, nu.mgz, talairach.xfm Does this error occur because I am using an old Freesurfer version? If this is the case which is the optimal version to run hippocampal segmentation? Should I process my whole data again with the newest version? Unfortunately I did not find any convincing answer from the posting list where I had the impression that version 5.1 is facing some problems regarding hippocampal segmentation. Thank you very much and kind regards, Lorenzo Pasquini___ 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] problem in building cortex mask
Dear freesurfers, I have a problem in creating masks of the left and right cerebral cortexes. The message "found 0 values in range" is displayed and an empty mask is created. This is surprising as I am able to build masks of the right and left hippocampi and entorhinal cortexes using the same command without any problems. Further the satistic file aseg.stats indicates me a huge amount of voxels in the cerebral cortexes. I am using the segmentation ID 3 for the left cerebral corex and 42 or 53 for the right cerebral cortex. I am surprised as well to find two different IDs for the same region, 42 comes from the aseg.stats file, 53 comes from the FreesurferColorLUT table. Wich ID is the right one to use?Why can I build masks of hippocampal regions but not of the cerebral cortexes? Thank you very much and kind regards, Lorenzo Pasquini___ 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.
