[Freesurfer] viewing certain regions
Hi! I want to view only certain segmented regions on one of our subject's brains. It seems like it should be simple but I am struggling to find the steps. I want to display only hippocampus, amygdala, medial orbitofrontal, lateral orbitofrontal, sulcus/gyri anterior cingulate, subcallosal gyrus, and rACC and cACC. How do I extract these labels so that I can only show just these regions on the brain? I extracted stats for these areas, but want to visually show the locations. Thank you, Courtney ___ 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] mri_segstats question
Hi Doug, Thanks again for your reply. One last question: The aseg.mgz file includes the cortex as well. If I want to extract the cortex from the aseg.mgz file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and subtract them, and then use the result in the mri_segstats command, or is there a different way? Thanks, Panos On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, Thanks for the quick reply! In addition: 1) The average intensity measure in the above example does not include the intensity of the skull, just everything inside, right? It includes all the structures that are segmented in seg. If there is not a skull segmentation, then it will not be in the output list. 2) Just to be clear on the purpose of including the segmentations in the command line: The segmentations only specify the areas of the brain that you would like to measure the intensity on, but besides that they don't provide any intensity info by themselves, would that be correct? That is the purpose of the --i flag, right? Correct doug Thanks again for your help, Panos On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS community, I had some questions regarding the mri_segstats command: 1) In the excludeid flag, are the ids the ones shown in the FreeSurferColorLUT.txt? Yes 2) In case I would like to measure the mean intensity of the orig file as outlined in the second example in https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats: mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum bert.aseg.sum --in $SUBJECTS_DIR/bert/mri/orig is the --seg flag necessary in order to calculate only the mean intensity within the skull, or does it serve another purpose? The seg defines the segmentations (eg, 17 is hippocampus) Thanks in advance, Panos ___ 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 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 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] mri_segstats question
If you want the volume of cortex, you should definitely not use aseg.mgz. aparc+aseg is better, but the best is to use the surface-based measure found in aseg.stats doug On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, Thanks again for your reply. One last question: The aseg.mgz file includes the cortex as well. If I want to extract the cortex from the aseg.mgz file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and subtract them, and then use the result in the mri_segstats command, or is there a different way? Thanks, Panos On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, Thanks for the quick reply! In addition: 1) The average intensity measure in the above example does not include the intensity of the skull, just everything inside, right? It includes all the structures that are segmented in seg. If there is not a skull segmentation, then it will not be in the output list. 2) Just to be clear on the purpose of including the segmentations in the command line: The segmentations only specify the areas of the brain that you would like to measure the intensity on, but besides that they don't provide any intensity info by themselves, would that be correct? That is the purpose of the --i flag, right? Correct doug Thanks again for your help, Panos On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS community, I had some questions regarding the mri_segstats command: 1) In the excludeid flag, are the ids the ones shown in the FreeSurferColorLUT.txt? Yes 2) In case I would like to measure the mean intensity of the orig file as outlined in the second example in https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats: mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum bert.aseg.sum --in $SUBJECTS_DIR/bert/mri/orig is the --seg flag necessary in order to calculate only the mean intensity within the skull, or does it serve another purpose? The seg defines the segmentations (eg, 17 is hippocampus) Thanks in advance, Panos ___ 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] ROI analysis in Matlab
It looks right. Make sure that you have specified self when you run mkanalysis-sess to make sure the analysis is on the subject's own anatomy where you have MT defined doug On 04/20/2014 08:35 AM, Reza Rajimehr wrote: Hi, For my dataset, it appears to be easier to do an ROI analysis in Matlab (instead of using funcroi commands). I just want to make sure the procedure described below is right: 1) I have a label/ROI on the right hemisphere surface of a subject (e.g. MT from the motion localizer). I convert it to a mask file (MT.mask.nii.gz). I load it to Matlab using MRIread. In an fMRI experiment, I have 3 conditions. For the right hemisphere vertices of the subject, I compute cespct.nii.gz for the contrasts of each condition vs. baseline (1_vs_0 , 2_vs_0 , 3_vs_0). Then I load the three cespct files to Matlab using MRIread. 3) For the vertices that are 1 in the MT.mask.nii.gz, I calculate the averaged cespct across those vertices, in each contrast. So I will have % signal change values for the three conditions. 4) I repeat this for all subjects and do statistics across subjects. Any comments? Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] rmanova contrast file error
you have an extra blank line in your contrast matrix On 04/19/2014 11:41 PM, Harry Hallock [hhal5...@uni.sydney.edu.au] wrote: Dear Experts, I am running a rmanova using FSGD file and mri_glmfit. I have done the mris_preproc step, and am currently trying to do the mri_glmfit step. I keep getting an error that appears to be related to the contrast files and matricies (highlighted in yellow below) I have also attched the FSGD file and a contrast file. Everything is in ASCII. The output from the command terminal is below: mri_glmfit --glmdir lh.rmanova --y lh.thickness.mgh --fsgd rmanova.fsgd doss --C tp1_vs_tp2.mtx --C tp1_vs_tp3.mtx --C tp2_vs_tp3.mtx --C tp_effect.mtx --C mean.mtx --surface fsaverage lh gdfReadHeader: reading rmanova.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 tp1_vs_tp2 0 0.840168 1 tp2_vs_tp3 0 0.766965 Class Means of each Continuous Variable 1 ECT_001 0. 0. 2 ECT_002 0. 0. 3 ECT_003 0. 0. 4 ECT_004 0. 0. 5 ECT_005 0. 0. 6 ECT_006 0. 0. 7 ECT_007 0. 0. 8 ECT_008 0. 0. 9 ECT_009 0. 0. 10 ECT_010 0. 0. 11 ECT_011 0. 0. 12 ECT_012 0. 0. 13 ECT_013 0. 0. 14 ECT_014 0. 0. 15 ECT_015 0. 0. 16 ECT_016 0. 0. 17 ECT_017 0. 0. 18 ECT_018 0. 0. 19 ECT_019 0. 0. 20 ECT_020 0. 0. 21 ECT_021 0. 0. 22 ECT_022 0. 0. 23 ECT_023 0. 0. 24 ECT_024 0. 0. INFO: gd2mtx_method is doss Reading source surface /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1 cmdline mri_glmfit --glmdir lh.rmanova --y lh.thickness.mgh --fsgd rmanova.fsgd doss --C tp1_vs_tp2.mtx --C tp1_vs_tp3.mtx --C tp2_vs_tp3.mtx --C tp_effect.mtx --C mean.mtx --surface fsaverage lh sysname Linux hostname fs-OptiPlex-755 machine i686 user fs FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/lh.thickness.mgh logyflag 0 usedti 0 FSGD rmanova.fsgd labelmask /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.rmanova IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.rmanova Loading y from /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/lh.thickness.mgh INFO: gd2mtx_method is doss Saving design matrix to lh.rmanova/Xg.dat Normalized matrix condition is 2.67942 Matrix condition is 32.198 Found 149955 points in label. Pruning voxels by thr: 0.00 Found 148274 voxels in mask Saving mask to lh.rmanova/mask.mgh Reshaping mriglm-mask... search space = 73670.427324 MatrixReadTxT: could not scan value [2][1] ERROR: loading C tp1_vs_tp2.mtx Any help would be greatly appreciated. Thanks, Harry *Harry Hallock*| MPhil Candidate Regenerative Neuroscience Group | Brain Mind Research Institute *THE UNIVERSITY OF SYDNEY* Room 408, Level 4, M02K | 94 Mallett St Camperdown | NSW | 2050| Australia *T +*61 2 9114 4138 F +61 9351 0930 *E *hhal5...@uni.sydney.edu.au*| W *www.rng.org.au ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_segstats question
Hi Doug, I'm sorry, what I meant to ask in the previous question is whether there is a way to come up with a segmentation volume for the mri_segstats command that is exactly like aseg.mgz but that does not include the cortex. The reason I'm asking is because by using the aseg.mgz volume in the --seg flag, you're also incorporating the intensity of the cortex when measuring the mean intensity of orig.mgz, but I wanted to see if there was a way to calculate the mean intensity of orig.mgz but without incorporating the intensity of the cortex. Thanks again, Panos If you want the volume of cortex, you should definitely not use aseg.mgz. aparc+aseg is better, but the best is to use the surface-based measure found in aseg.stats doug On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, Thanks again for your reply. One last question: The aseg.mgz file includes the cortex as well. If I want to extract the cortex from the aseg.mgz file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and subtract them, and then use the result in the mri_segstats command, or is there a different way? Thanks, Panos On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, Thanks for the quick reply! In addition: 1) The average intensity measure in the above example does not include the intensity of the skull, just everything inside, right? It includes all the structures that are segmented in seg. If there is not a skull segmentation, then it will not be in the output list. 2) Just to be clear on the purpose of including the segmentations in the command line: The segmentations only specify the areas of the brain that you would like to measure the intensity on, but besides that they don't provide any intensity info by themselves, would that be correct? That is the purpose of the --i flag, right? Correct doug Thanks again for your help, Panos On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS community, I had some questions regarding the mri_segstats command: 1) In the excludeid flag, are the ids the ones shown in the FreeSurferColorLUT.txt? Yes 2) In case I would like to measure the mean intensity of the orig file as outlined in the second example in https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats: mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum bert.aseg.sum --in $SUBJECTS_DIR/bert/mri/orig is the --seg flag necessary in order to calculate only the mean intensity within the skull, or does it serve another purpose? The seg defines the segmentations (eg, 17 is hippocampus) Thanks in advance, Panos ___ 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] RAS to MNI coordinate conversion function?
Hi John, please remember to post to the list. thanks! Yes, that should work. Use read read_surf.m to get the proper coordinates. doug On 04/20/2014 08:08 PM, John Pyles wrote: Hi Doug, Thanks so much for the reply. I had looked through the wiki on coordinates but because I'm not a big Freesurfer user was unsure which was the correct transformation. It seems like for what I need to do the example below is appropriate? So in theory I could write a Matlab function using the calculation below correct? Thanks again. Best, John 2. I have an RAS point on the surface (tkrR tkrA tkrS) (Vertex RAS from tksurfer) and want to compute the MNI305 RAS that corresponds to this point: MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' TalXFM: subject/orig/transforms/talairach.xfm Norig: mri_info --vox2ras orig.mgz Torig: mri_info --vox2ras-tkr orig.mgz __ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University email: jpy...@cmu.edu phone: 206.552.0107 __ On Fri, 18 Apr 2014, Douglas Greve wrote: There is not a simple function, but you can look at our wiki page on coordinate systems. There are some examples there on tranforming from one coordinate to another doug On 4/18/14 2:40 PM, John Pyles wrote: Hi, I am not a heavy Freesurfer user and I haven't had good luck figuring this out through the FreeSurfer documentation and I thought an expert might have a fast answer. If anyone has an easy solution it would be very much appreciated. While I use FreeSurfer for automatic segmentation, I don't normally use if for analysis. However for an ECoG project I'm using parts of FreeSurfer to aid in electrode coregistration. Basically the issue is that I have electrode coordinates in what I believe are FreeSurfer RAS space and I need to convert them to MNI space. I have many of these electrode coordinates for each subject so I need a FreeSurfer or Matlab function to automate this process. Is there a simple way to do this? The *very* kludgy way I figured out how to do this manually is as follows (I'm sure this is going to seem very dumb to a FreeSurfer user, but I needed a quick solution that worked for a figure). 1) Enter the coordinate output from my electrode coregistration routines manually into the RAS field in Freeview. 2) Take the brain volume coordinates (all positive) in Freeview and enter them into the Volume Coordinate field in TkMedit. 3) Copy the TAL coordinates output in MkEdit when the brain volume coordinate is entered. 4) Convert the TAL coordinates to MNI in Matlab with tal2mni.m It seems like there should be a simple function to do this coordinate conversion using the transformation info from recon-all that I'm assuming both Freeview and TkMedit use, but I can't seem to find it? Any help would be appreciated. Thanks again! Best, John __ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University __ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] R: Filipping issue
Hi Paola, please remember to post to the list and not to us personally. thanks! I would still use the xhemi tools for this. If you have N subjects, you will get 2*N surfaces aligned to the fsaverage_sym atlas. You can then just pick the ones you want to analyze further doug On 04/22/2014 08:34 AM, Paola Valsasina wrote: Dear Doug, We have followed your suggestion and we performed the recon-all analysis for all study subjects (till autorecon3) on non-flipped images. I am now reading the instructions on the wiki about the xhemi tool, but I am not 100% sure they apply to our case. The wiki instructions describe a comparison between LH and RH within subjects (i.e., an analysis of cortical asymmetry), whereas we would like simply to L-R flip the final surfaces of patients having a RH damage, so that all patients have the damage in the LH. Then, we would like to compare them with control subjects. For this purpose, is it sufficient to register the patients lesioned in the RH to the symmetric template with the --xhemi option? (i.e. surfreg --s subject_name --t fsaverage_sym --xhemi --rh --lh) Then, how do we perform final statistical analysis? Thank you in advance for any suggestion! Kind regards Paola Paola Valsasina, MSc Research Fellow Neuroimaging Research Unit (Director Prof. M. Filippi) Institute of Experimental Neurology, Division of Neuroscience, Scientific Institute and University Vita-Salute San Raffaele Via Olgettina 60, 20132 Milan, Italy -- IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO PERCHE' QUI LA RICERCA DIVENTA CURA. CF 07636600962 SE NON QUI, DOVE? Info: 5xmi...@hsr.it - http://www.5xmille.org/ Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com -Messaggio originale- Da: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Per conto di Douglas N Greve Inviato: giovedì 13 febbraio 2014 21.50 A: freesurfer@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] Filipping issue Definitely #2. You should use the xhemi tools http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi First run them through recon-all as normal, then follow the steps on the wiki. Contact the list again to get instructions for the final analysis. doug On 02/13/2014 08:23 AM, Paola Valsasina wrote: Dear List, we are starting the analysis of cortical thickness for a group of patients who have only one side affected. The majority of patients have the left hemisphere affected, but some patients have the right hemisphere affected. In order to do a group analysis, we would like to flip the images of some patients, so that the affected side is left for all subjects. Which is the best way to do this: 1)flip the 001.mgz volume and perform the entire recon-all pipeline with flipped images; or 2)perform the recon-all pipeline with the non-flipped volumes and flip only the final surfaces for statistical purposes? Thank you for any suggestion Kind regards Paola ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] convert volume-based mni152 space into fsaverage surface space(MNI305)
Use mri_vol2surf with $FREESURFER_HOME/average/mni152.register.dat On 04/21/2014 10:20 PM, charujing123 wrote: Hi FS experts and users, I created a mask volume, whose space is in MNI152 space. And I want to convert this volume into surface-based in fsaverage. How can I realize this? Thanks All the best. Rujing Zha 2014-04-22 charujing123 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] viewing certain regions
Use mri_binarize with the --match option to create a mask of the regions you want. Then use mri_mask applied to aparc+aseg to create a new volume with only the regions you want doug On 04/22/2014 09:06 AM, Courtney Haswell wrote: Hi! I want to view only certain segmented regions on one of our subject's brains. It seems like it should be simple but I am struggling to find the steps. I want to display only hippocampus, amygdala, medial orbitofrontal, lateral orbitofrontal, sulcus/gyri anterior cingulate, subcallosal gyrus, and rACC and cACC. How do I extract these labels so that I can only show just these regions on the brain? I extracted stats for these areas, but want to visually show the locations. Thank you, Courtney ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] 2 available spots in Boston FreeSurfer course
Hi Andrew, Yes you’re down for a spot. Yours wasn’t one of the two :). Allison On Apr 18, 2014, at 3:23 PM, Andrew Gerber gerb...@nyspi.columbia.edu wrote: Dear Allison, You have me down for a slot, right? I don't want to miss it! :-) Best, Andrew -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Allison Stevens Sent: Friday, April 18, 2014 3:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] 2 available spots in Boston FreeSurfer course We have had some last minute drop outs and there are now 2 spots available in the upcoming Boston FreeSurfer course (May 5-7th). If you would like to sign up for these spots, please register here: https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.8263.cgi Note that credit card cannot be used to pay for the course. Also, this course will not have the diffusion analysis component (it will focus on fMRI analysis). Allison ___ 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] R: R: Filipping issue
Sorry, I didn't note I was replying to you only.. Anyway, thank you for the reply! So I will apply the command I mentioned to you in my previous e-mail to create flipped RH and LH surfaces for the subjects with the right hemisphere affected. Should I register to the fsaverage_sym atlas also the subjects I don't want to flip (i.e., those with the left hemisphere affected), to pool them together in the statistic with the flipped subjects? Thank you again Paola Paola Valsasina, MSc Research Fellow Neuroimaging Research Unit (Director Prof. M. Filippi) Institute of Experimental Neurology, Division of Neuroscience, Scientific Institute and University Vita-Salute San Raffaele Via Olgettina 60, 20132 Milan, Italy -- IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO PERCHE' QUI LA RICERCA DIVENTA CURA. CF 07636600962 SE NON QUI, DOVE? Info: 5xmi...@hsr.it - http://www.5xmille.org/ Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com -Messaggio originale- Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Inviato: martedì 22 aprile 2014 17.56 A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu Oggetto: Re: R: [Freesurfer] Filipping issue Hi Paola, please remember to post to the list and not to us personally. thanks! I would still use the xhemi tools for this. If you have N subjects, you will get 2*N surfaces aligned to the fsaverage_sym atlas. You can then just pick the ones you want to analyze further doug On 04/22/2014 08:34 AM, Paola Valsasina wrote: Dear Doug, We have followed your suggestion and we performed the recon-all analysis for all study subjects (till autorecon3) on non-flipped images. I am now reading the instructions on the wiki about the xhemi tool, but I am not 100% sure they apply to our case. The wiki instructions describe a comparison between LH and RH within subjects (i.e., an analysis of cortical asymmetry), whereas we would like simply to L-R flip the final surfaces of patients having a RH damage, so that all patients have the damage in the LH. Then, we would like to compare them with control subjects. For this purpose, is it sufficient to register the patients lesioned in the RH to the symmetric template with the --xhemi option? (i.e. surfreg --s subject_name --t fsaverage_sym --xhemi --rh --lh) Then, how do we perform final statistical analysis? Thank you in advance for any suggestion! Kind regards Paola Paola Valsasina, MSc Research Fellow Neuroimaging Research Unit (Director Prof. M. Filippi) Institute of Experimental Neurology, Division of Neuroscience, Scientific Institute and University Vita-Salute San Raffaele Via Olgettina 60, 20132 Milan, Italy -- IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO PERCHE' QUI LA RICERCA DIVENTA CURA. CF 07636600962 SE NON QUI, DOVE? Info: 5xmi...@hsr.it - http://www.5xmille.org/ Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com -Messaggio originale- Da: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Per conto di Douglas N Greve Inviato: giovedì 13 febbraio 2014 21.50 A: freesurfer@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] Filipping issue Definitely #2. You should use the xhemi tools http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi First run them through recon-all as normal, then follow the steps on the wiki. Contact the list again to get instructions for the final analysis. doug On 02/13/2014 08:23 AM, Paola Valsasina wrote: Dear List, we are starting the analysis of cortical thickness for a group of patients who have only one side affected. The majority of patients have the left hemisphere affected, but some patients have the right hemisphere affected. In order to do a group analysis, we would like to flip the images of some patients, so that the affected side is left for all subjects. Which is the best way to do this: 1)flip the 001.mgz volume and perform the entire recon-all pipeline with flipped images; or 2)perform the recon-all pipeline with the non-flipped volumes and flip only the final surfaces for statistical purposes? Thank you for any suggestion Kind regards Paola ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ The information in this e-mail is intended only for the person to whom it is addressed. If you believe
Re: [Freesurfer] mri_segstats question
You can just do it in matlab, somethhing like
a = MRIread('aparc+aseg.mgz');
ind = find(a.vol 999);
a.vol(ind) = 0;
MRIwrite(a,'nocortex.mgz')
On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
I'm sorry, what I meant to ask in the previous question is whether there
is a way to come up with a segmentation volume for the mri_segstats
command that is exactly like aseg.mgz but that does not include the
cortex. The reason I'm asking is because by using the aseg.mgz volume in
the --seg flag, you're also incorporating the intensity of the cortex when
measuring the mean intensity of orig.mgz, but I wanted to see if there was
a way to calculate the mean intensity of orig.mgz but without
incorporating the intensity of the cortex.
Thanks again,
Panos
If you want the volume of cortex, you should definitely not use
aseg.mgz. aparc+aseg is better, but the best is to use the surface-based
measure found in aseg.stats
doug
On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
Thanks again for your reply. One last question: The aseg.mgz file
includes
the cortex as well. If I want to extract the cortex from the aseg.mgz
file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and
subtract them, and then use the result in the mri_segstats command, or
is
there a different way?
Thanks,
Panos
On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
Thanks for the quick reply! In addition:
1) The average intensity measure in the above example does not include
the
intensity of the skull, just everything inside, right?
It includes all the structures that are segmented in seg. If there is
not a skull segmentation, then it will not be in the output list.
2) Just to be clear on the purpose of including the segmentations in
the
command line: The segmentations only specify the areas of the brain
that
you would like to measure the intensity on, but besides that they
don't
provide any intensity info by themselves, would that be correct? That
is
the purpose of the --i flag, right?
Correct
doug
Thanks again for your help,
Panos
On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote:
Hi FS community,
I had some questions regarding the mri_segstats command:
1) In the excludeid flag, are the ids the ones shown in the
FreeSurferColorLUT.txt?
Yes
2) In case I would like to measure the mean intensity of the orig
file
as
outlined in the second example in
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats:
mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt
--nonempty --excludeid 0 --sum bert.aseg.sum
--in $SUBJECTS_DIR/bert/mri/orig
is the --seg flag necessary in order to calculate only the mean
intensity
within the skull, or does it serve another purpose?
The seg defines the segmentations (eg, 17 is hippocampus)
Thanks in advance,
Panos
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Re: [Freesurfer] R: R: Filipping issue
You can register just the hemisphere you want to fsaverage_sym. But if you have a subject whose right hemi you want, you would run the surfreg with --rh, but later you would specify that you want the lh of subject/xhemi doug On 04/22/2014 12:04 PM, Paola Valsasina wrote: Sorry, I didn't note I was replying to you only.. Anyway, thank you for the reply! So I will apply the command I mentioned to you in my previous e-mail to create flipped RH and LH surfaces for the subjects with the right hemisphere affected. Should I register to the fsaverage_sym atlas also the subjects I don't want to flip (i.e., those with the left hemisphere affected), to pool them together in the statistic with the flipped subjects? Thank you again Paola Paola Valsasina, MSc Research Fellow Neuroimaging Research Unit (Director Prof. M. Filippi) Institute of Experimental Neurology, Division of Neuroscience, Scientific Institute and University Vita-Salute San Raffaele Via Olgettina 60, 20132 Milan, Italy -- IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO PERCHE' QUI LA RICERCA DIVENTA CURA. CF 07636600962 SE NON QUI, DOVE? Info: 5xmi...@hsr.it - http://www.5xmille.org/ Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com -Messaggio originale- Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Inviato: martedì 22 aprile 2014 17.56 A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu Oggetto: Re: R: [Freesurfer] Filipping issue Hi Paola, please remember to post to the list and not to us personally. thanks! I would still use the xhemi tools for this. If you have N subjects, you will get 2*N surfaces aligned to the fsaverage_sym atlas. You can then just pick the ones you want to analyze further doug On 04/22/2014 08:34 AM, Paola Valsasina wrote: Dear Doug, We have followed your suggestion and we performed the recon-all analysis for all study subjects (till autorecon3) on non-flipped images. I am now reading the instructions on the wiki about the xhemi tool, but I am not 100% sure they apply to our case. The wiki instructions describe a comparison between LH and RH within subjects (i.e., an analysis of cortical asymmetry), whereas we would like simply to L-R flip the final surfaces of patients having a RH damage, so that all patients have the damage in the LH. Then, we would like to compare them with control subjects. For this purpose, is it sufficient to register the patients lesioned in the RH to the symmetric template with the --xhemi option? (i.e. surfreg --s subject_name --t fsaverage_sym --xhemi --rh --lh) Then, how do we perform final statistical analysis? Thank you in advance for any suggestion! Kind regards Paola Paola Valsasina, MSc Research Fellow Neuroimaging Research Unit (Director Prof. M. Filippi) Institute of Experimental Neurology, Division of Neuroscience, Scientific Institute and University Vita-Salute San Raffaele Via Olgettina 60, 20132 Milan, Italy -- IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO PERCHE' QUI LA RICERCA DIVENTA CURA. CF 07636600962 SE NON QUI, DOVE? Info: 5xmi...@hsr.it - http://www.5xmille.org/ Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com -Messaggio originale- Da: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Per conto di Douglas N Greve Inviato: giovedì 13 febbraio 2014 21.50 A: freesurfer@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] Filipping issue Definitely #2. You should use the xhemi tools http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi First run them through recon-all as normal, then follow the steps on the wiki. Contact the list again to get instructions for the final analysis. doug On 02/13/2014 08:23 AM, Paola Valsasina wrote: Dear List, we are starting the analysis of cortical thickness for a group of patients who have only one side affected. The majority of patients have the left hemisphere affected, but some patients have the right hemisphere affected. In order to do a group analysis, we would like to flip the images of some patients, so that the affected side is left for all subjects. Which is the best way to do this: 1)flip the 001.mgz volume and perform the entire recon-all pipeline with flipped images; or 2)perform the recon-all pipeline with the non-flipped volumes and flip only the final surfaces for statistical purposes? Thank you for any suggestion Kind regards Paola ___ 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:
Re: [Freesurfer] 2 available spots in Boston FreeSurfer course
Good! :-) See you soon. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Allison Stevens Sent: Tuesday, April 22, 2014 12:02 PM To: Freesurfer support list Subject: Re: [Freesurfer] 2 available spots in Boston FreeSurfer course Hi Andrew, Yes you're down for a spot. Yours wasn't one of the two :). Allison On Apr 18, 2014, at 3:23 PM, Andrew Gerber gerb...@nyspi.columbia.edu wrote: Dear Allison, You have me down for a slot, right? I don't want to miss it! :-) Best, Andrew -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Allison Stevens Sent: Friday, April 18, 2014 3:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] 2 available spots in Boston FreeSurfer course We have had some last minute drop outs and there are now 2 spots available in the upcoming Boston FreeSurfer course (May 5-7th). If you would like to sign up for these spots, please register here: https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.8263.cgi Note that credit card cannot be used to pay for the course. Also, this course will not have the diffusion analysis component (it will focus on fMRI analysis). Allison ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_segstats question
That is great,
Thanks a lot, Doug!
You can just do it in matlab, somethhing like
a = MRIread('aparc+aseg.mgz');
ind = find(a.vol 999);
a.vol(ind) = 0;
MRIwrite(a,'nocortex.mgz')
On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
I'm sorry, what I meant to ask in the previous question is whether there
is a way to come up with a segmentation volume for the mri_segstats
command that is exactly like aseg.mgz but that does not include the
cortex. The reason I'm asking is because by using the aseg.mgz volume in
the --seg flag, you're also incorporating the intensity of the cortex
when
measuring the mean intensity of orig.mgz, but I wanted to see if there
was
a way to calculate the mean intensity of orig.mgz but without
incorporating the intensity of the cortex.
Thanks again,
Panos
If you want the volume of cortex, you should definitely not use
aseg.mgz. aparc+aseg is better, but the best is to use the
surface-based
measure found in aseg.stats
doug
On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
Thanks again for your reply. One last question: The aseg.mgz file
includes
the cortex as well. If I want to extract the cortex from the aseg.mgz
file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and
subtract them, and then use the result in the mri_segstats command, or
is
there a different way?
Thanks,
Panos
On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
Thanks for the quick reply! In addition:
1) The average intensity measure in the above example does not
include
the
intensity of the skull, just everything inside, right?
It includes all the structures that are segmented in seg. If there is
not a skull segmentation, then it will not be in the output list.
2) Just to be clear on the purpose of including the segmentations in
the
command line: The segmentations only specify the areas of the brain
that
you would like to measure the intensity on, but besides that they
don't
provide any intensity info by themselves, would that be correct?
That
is
the purpose of the --i flag, right?
Correct
doug
Thanks again for your help,
Panos
On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote:
Hi FS community,
I had some questions regarding the mri_segstats command:
1) In the excludeid flag, are the ids the ones shown in the
FreeSurferColorLUT.txt?
Yes
2) In case I would like to measure the mean intensity of the orig
file
as
outlined in the second example in
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats:
mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt
--nonempty --excludeid 0 --sum bert.aseg.sum
--in $SUBJECTS_DIR/bert/mri/orig
is the --seg flag necessary in order to calculate only the mean
intensity
within the skull, or does it serve another purpose?
The seg defines the segmentations (eg, 17 is hippocampus)
Thanks in advance,
Panos
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] viewing certain regions
HI Courtney, please post to the list. Thanks! Get the codes from $FREESURFER_HOME/FreeSurferColorLUT.txt. Also, you can use multiple numbers to match all the ROIs you want at once (if that is what you want). Eg, --match 2 26 17 doug On 04/22/2014 03:16 PM, Courtney Haswell wrote: Thanks for the reply. I was able to make the hippocampus and amygdala masks easily, but was having some trouble for the other ones. Looking in the aparc.annot.ctab file, I see that caudalanteriorcingulate is labeled 2 and rostralanteriorcingulate is 26. So then is this the correct way to get the ROI extracted: mri_binarize --i $SUBJDIR/aparc+aseg.mgz --o $ROIDIR/3_rostralACC.mgz --match 26 mri_binarize --i $SUBJDIR/aparc+aseg.mgz --o $ROIDIR/3_caudalACC.mgz --match 2 I also did the caudal ACC (that is in aparc.annot) the same way but that ROI covers all of the white matter in the right hemisphere so I think I did something wrong. mri_binarize --i $SUBJDIR/aparc+aseg.mgz --o $ROIDIR/3_caudalACC.mgz --match 2 mri_mask $SUBJDIR/aparc+aseg.mgz $ROIDIR/3_caudalACC.mgz $ROIDIR/acc_mask5.mgz Thank you, Courtney Use mri_binarize with the --match option to create a mask of the regions you want. Then use mri_mask applied to aparc+aseg to create a new volume with only the regions you want doug On 04/22/2014 09:06 AM, Courtney Haswell wrote: Hi! I want to view only certain segmented regions on one of our subject's brains. It seems like it should be simple but I am struggling to find the steps. I want to display only hippocampus, amygdala, medial orbitofrontal, lateral orbitofrontal, sulcus/gyri anterior cingulate, subcallosal gyrus, and rACC and cACC. How do I extract these labels so that I can only show just these regions on the brain? I extracted stats for these areas, but want to visually show the locations. Thank you, Courtney -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon all problem
Hi Danielle what does it look like withouth the FLAIR postprocessing? And what FLAIR sequence are you using? We have only ever used the T2-space FLAIR and have been told that it works great with that, but not as well with other FLAIR variants. cheers Bruce On Tue, 22 Apr 2014, Danielle Miller wrote: Hi Freesurfer Experts, I seem to be having some difficulty with reconing a healthy young adult. I have tried running this on multiple different computers and multiple different versions (5.3 and 5.1) and all return the same weird recon (see attached image). I have used the same sequence and commands on another subject and the recon returned fine. This participant did not have excess motion and the orig.mgz file looks fine. Please let me know if there is any more information I could provide that would be of use. Commands used: 5.3: recon-all -all -FLAIR (FLAIR image) -subjid (SUBJID) -FLAIRpial -hippo-subfields recon-all -all -subjid (SUBJID) 5.1: recon-all -all -subjid (SUBJID) -hippo-subfields recon-all -all -subjid (SUBJID) Thanks, Danielle Miller -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130 ___ 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] CUDA PC build
Hi, Trying to build a CUDA enabled PC for the lab to do processing for a variety of neuroimaging programs including Freesurfer and FSL. Want to know input from others about the 'recommended' PC and what the 'standard' is based on the current PC prices and technology. Sample build is from NCIX Canada, if curious. SKU Description Price Amount 84500 ASUS Z87-A ATX LGA1150 Z87 DDR3 3PCI-E16 2PCI-E1 2PCI CrossFireX/SLI SATA3 USB3.0 HDMI Motherboard [Reg. $159.99] $154.99 $154.99 93608 ADATA Xpg V1.0 16GB DDR3-1600 CL9-9-9-24 2X8GB Dual Channel Memory Kit Black [Reg.$189.99] $149.99 $149.99 82953 ASUS DRW-24F1ST 24X SATA DVD Writer Black $24.98 $24.98 65701 Seagate Barracuda 1TB 7200RPM 64MB SATA 6Gbps 3.5in Internal Hard Drive - OEM [Reg. $73.44] $64.99 $64.99 76367 ASUS GeForce GTX 660 OC DirectCU 1020MHZ 2GB 6.0GHZ GDDR5 2xDVI HDMI DisplayPort PCI-E Video Card $229.99 $459.98 81327 Intel Core i5 4670K Unlocked Quad Core 3.4GHZ Processor LGA1150 Haswell 6MB Cache Retail [Reg. $269.98] $249.99 $249.99 38650 Corsair Professional HX850W 850W ATX 12V 70A 24PIN ATX Modular Power Supply Active PFC 140mm Fan $169.98 $169.98 67326 Antec Three Hundred Two Mid Tower Gaming Case 302 ATX 3X5.25 6X3.5INT No PS Front USB3.0 Audio [Reg. $77.98] $69.99 $69.99 In short -- runs with 16 Gb RAM, 3.4 GHz Quad core, with 2 GTX 660s in SLI. Final quote comes out to $1506 CAD. This is my first time attempting to build a PC of this type, so I still have tons of questions regarding minor details. I think spec wise the computer is good, unless others have recommendations from previous experience. Most likely will be running a flavour of Linux on this rig. Any suggestions for what the 'standard' for this build would be? I'm thinking CentOS based on older webmail threads, but I would prefer Ubuntu if possible. I would also like it to be user friendly so the technologically challenged researchers can get the software up and running. Is there anything else I should think about before I order? I want to make sure I have all of my bases covered before ordering and getting this rig going. Regards, - Bryan Chiu ___ 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] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?
Hi Sabin, I have not been able to definitively track down the source of the negative area, but I have verified a couple of things. There is only negative area in a couple of vertices and they are in the medial wall. Our current development version does not result in negative area when I run it on your data, so what ever is happening has been fixed. In general, the area from the current development version is very close to that of what you have, so I think the negative area can be ignored. doug On 04/17/2014 12:47 PM, sabin khadka wrote: Hi all, I ran mri_surf2surf and then mris_convert to get vertexwise thickness and surface area values in ascii files. I found that some vertices had negative values of surface area for few subjects. Should not surface area values be positive only? -Sabin On Thursday, April 17, 2014 10:30 AM, sabin khadka sabink...@yahoo.com wrote: Ahh. Great. Thanks you very much for the information. I ran mri_surf2surf and then mris_convert to get thickness and surface area vertex wise values. I found that some vertices had negative values of surface area for few subjects. Should not surface area values be positive only? -Sabin On Thursday, April 17, 2014 10:10 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: yes, you can use mri_surf2surf first to map them to fsaverage, then convert them to ascii On Thu, 17 Apr 2014, sabin khadka wrote: Hi Bruce, Thanks for the reply. I was wondering if I have to somehow resample or map to fsaverage so as to have same # of vertices across all subjects. I tried using mris_convert as you suggested above but I can see that different subjects have different #of vertices. Thanks for help. -Sabin On Thursday, April 17, 2014 9:29 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Sabin mris_convert can convert binary curvature format files to ascii ones if the output file has the extension asc. Something like: mris_convert -c lh.thickness lh.orig lh.thickness.asc this will give you a 5 column ascii file in the format vertex index x y z thickness cheers Bruce On Thu, 17 Apr 2014, sabin khadka wrote: Hi all, I want to extract to extract thickness, area and lgi values vertex wise in ascii files for group of subjects. Could anyone suggest me on how to do it. Thank you for your help. -Sabin 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3
Hi, I am still having some concerns using mri_convert on Skyra volumes that I'm hoping can please be addressed. On this occasion I have used mri_convert to convert a single dicom file to nifti from a volume collected on a siemens Skyra scanner using Freesurfer5.3 on CentOS5.7. When viewing this nifti image using tkmedit it appears 'cut-up' over many sagittal slices (please see attached) rather than the whole image appearing on one plane. Not sure if this is an issue with tkmedit or mri_convert? This problem persists if i convert the entire volume, with this 'cutting' appearing as vertical lines in the image. This is also the case when using the new mri_convert patch for OS X. Lastly, I can upload a dicom file if needed. Thanks, Paul Screenshot_crop.pdf Description: Binary data ___ 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.
