Re: [Freesurfer] correction for field dishomogeneity
Hi Clelia yes, we correct for field inhomogeneity. Presumably they mean the B1 receive field, which is what is typically meant in structurals. If they mean B0, we don't typically correct (nor do most people for structural imaging - this is more of an issue for diffusion and functional MRI). cheers Bruce On Fri, 3 Jul 2015, clelia pellicano wrote: Dear experts, I was wondering how freesurfer corrects for field dishomogeneity. As long as I know, it's automatically done by the software . My concern is because a reviewer has made this comment (please find it below): Authors used an old 3 T MRI without using the appropriate pipeline provided by freesurfer to correct for field dysomogeneity We have run the standard pipeline provided to derive measures of cortical thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ). Here the MRI protocol used: All participants were scanned on a 3-Tesla Philips Intera whole-body MRI scanner. A T1-weighted three-dimensional magnetization-prepared rapid acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition: 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired. Any clue about? Thank you in advance. BW Clelia . Clelia Pellicano, MDPhD Student in Clinical and Experimental Neurosciences and Psychiatry, Department of Neuroscience, Mental Health and Sensory Organs, NESMOS, Sapienza University Via di Grottarossa 1035, 00189 Rome, Italy phone +390633775579 fax +390633775900 Research Neurologist Department of Clinical and Experimental Neurology Santa Lucia Foundation IRCSS Via Ardeatina 306, 00179, Rome, Italy ___ 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] longitudinal analysis
Dear Freesurfer experts In the command long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR, Do-avg will compute the temporal average. I do not quite understand the temporal average Is the average of baseline and followup thicknesses? Best regards, Yawu ___ 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] correction for field dishomogeneity
Hi Bruce, thank you for your reply. Do you have any idea about what they could mean saying without using the appropriate pipeline provided by freesurfer? Thanks BW C Il giorno 03/lug/2015 15:32, Bruce Fischl fis...@nmr.mgh.harvard.edu ha scritto: Hi Clelia yes, we correct for field inhomogeneity. Presumably they mean the B1 receive field, which is what is typically meant in structurals. If they mean B0, we don't typically correct (nor do most people for structural imaging - this is more of an issue for diffusion and functional MRI). cheers Bruce On Fri, 3 Jul 2015, clelia pellicano wrote: Dear experts, I was wondering how freesurfer corrects for field dishomogeneity. As long as I know, it's automatically done by the software . My concern is because a reviewer has made this comment (please find it below): Authors used an old 3 T MRI without using the appropriate pipeline provided by freesurfer to correct for field dysomogeneity We have run the standard pipeline provided to derive measures of cortical thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ). Here the MRI protocol used: All participants were scanned on a 3-Tesla Philips Intera whole-body MRI scanner. A T1-weighted three-dimensional magnetization-prepared rapid acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition: 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired. Any clue about? Thank you in advance. BW Clelia . Clelia Pellicano, MDPhD Student in Clinical and Experimental Neurosciences and Psychiatry, Department of Neuroscience, Mental Health and Sensory Organs, NESMOS, Sapienza University Via di Grottarossa 1035, 00189 Rome, Italy phone +390633775579 fax +390633775900 Research Neurologist Department of Clinical and Experimental Neurology Santa Lucia Foundation IRCSS Via Ardeatina 306, 00179, Rome, Italy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] unique label from volume / surface ROIs
Hi Martin at the end of recon-all we correct the volume-based segmentations with the surfaces, so the aparc*.mgz files should be pretty accurate cheers Bruce On Thu, 2 Jul 2015, Martin Hebart wrote: Hi Doug, Thanks a lot. But aren't the aparc.a2009s+aseg.mgz the volume-based ROIs and aren't they less accurate than the surface-based ones? Best, Martin Am 02.07.2015 14:47 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: I would just use the 2nd command since aparc.a2009s+aseg.mgz will have already resolved the issues of overlap that you mention. doug On 07/02/2015 04:07 AM, Martin Hebart wrote: Here's the exact code that I used: surface: mri_label2vol --annot aparc.a2009s.annot --regheader $1/$2/mri/orig.mgz --o $1/$2/roi/mask_lh.nii --temp $1/$2/mri/orig.mgz --subject $2 --hemi lh --proj frac 0 1 .1 same for the right hemisphere. volumetric: mri_label2vol --seg $1/$2/mri/aparc.a2009s+aseg.mgz --regheader $1/$2/mri/orig.mgz --o $1/$2/roi/mask_vol.nii --temp $1/$2/mri/orig.mgz --subject $2 Cheers, Martin 2015-07-01 23:38 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: How did you create the ROIs? On 07/01/2015 12:25 PM, Martin Hebart wrote: Dear members of the list, I'm new to Freesurfer, so please excuse me asking possibly basic questions. I have spent quite some time on the wiki and searching through the emails before writing to the list, but I might have missed some important information. I would like to work on anatomical ROIs created based on Freesurfer's surface-based and volumetric ROIs and continue working with them in nifti format (e.g. for SPM). If I understand it correctly, the surface-based ROIs should take into account the individual subject's anatomy better than the volumetric ROIs would. At the same time, for subcortical regions it is necessary to use volumetric ROIs. I did recon -all, followed by extracting all surface ROIs using mri_label2vol --annot aparc.a2009s.annot and the volumetric ROIs using mri_label2vol --seg aparc.a2009s+aseg.mgz . Finally, I manually removed all cortical labels from the volumetric ROIs. Now when looking at the ROIs, they overlap slightly, both between left and right hemisphere (roughly 150 voxels), and between the hemispheres and the subcortical regions (roughly 300 voxels). Is there a way I can assign the masks volumes a unique label? I was considering removing these voxels, but ideally I would just keep them in and use the label with the highest probability. Or is there an alternative suggestion that makes more sense (e.g. rather attributing overlapping regions to subcortical regions)? Thanks a lot in advance for your reply! Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 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
Re: [Freesurfer] recon-all: Same MRI, different execution tame
There are known and justifiable reason for potential differences in iteration count and run time of the code, potentially related to, but not limited to, random seed and convergence. But the case you demonstrate below is a bit extreme. And past experience running that code makes me dubious of the claim. Did you only perform 2 tests? Did the computation time for additional tests continue to demonstrate that variability? Are you sure IO variability (for whatever reason) can't account for the difference in runtime, while actual CPU time is the same? Nonetheless I will investigate by running that binary on some of our many datasets to see if I can replicate such an instance. -Zeke On Jul 2, 2015, at 3:45 AM, Jordi Delgado jordi...@pic.es wrote: Dear all, I'm performing a study about the variability of the execution time of recon-all. I noticed that the execution of recon-all in Freesurfer 5.3 for two identical MRIs (two copies of the same MRI), takes different execution time. I'm performing the execution using GPUs capability, but the same is happening for the CPU-only executions. Checking the output logs I found that in for example CA Reg, the number of the iterations is different, what's the main source of this variability? I guess that maybe It is related to some random seeds used and the convergence of the implemented methods. Am I right? CA Reg example: Execution Time 1 - Subject 1: 00:25:23 Execution Time 2 - Subject 1: 00:32:14 In both cases the computing node was used exclusively used for the recon-all execution. Did you measured the percentage of this variability? Can we extract some measures to compare the performed work on each execution? I'm thinking on the number of GPU kernels executed, the number of the iterations of the methods... Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ 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] tutorial materials
Hi, freesurfer experts: I am a newer to study freesurfer. I have completed recon-all for individual analysis. Next I want to study group analysis. I noticed there is a qdec folder under group_analysis_tutorial, I go into qdec folder and check the content of qdec.table.dat with cat command. I saw five columns data as followings: fsid gender age Left-Hippocampus Right-Hippocampus 140 Female 18 * 4214 4190* 049 Male194543 4153 141 Female 203896 3741 084 Male214804 4722 021 Male224021 3969 093 Female 223603 3597 080 Male233722 4645 ... My question is where does the data of Left-Hippocampus Right-Hippocampus come from? I checked the individual data from 140, 049, 141 I entered into /group_analysis_tutorial/140/stats/ and check the content of *aseg.stats *using cat aseg.stats, and I noticed tha Left-Hippocampus is *3851,* Right-Hippocampus is *4026*. all the data from other individuals aren't equal the data of Left-H and Right-H in qdec.table.dat. I am not sure what is the reason? Or could you please tell me where does the data of Left-H or Right-H come from? Thank you. Cheers. Yanmei ___ 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] how to make ROI using surface
Hi Bruce, Can you tell me how I can use mis_compute_layer_fractions ? I found it in dev_binary in http://ftp.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/snowleopard-i686/ http://ftp.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/snowleopard-i686/. Thanks! Yun On Jul 2, 2015, at 14:39, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: they are binaries. What version of FreeSurfer do you have, and what hardware/software environment? On Thu, 2 Jul 2015, Yun Wang wrote: I could not find the function, can you tell me why and how I use this function? Thanks! On Jul 2, 2015, at 14:30, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Yun Wang if you've run mris_expand you will need to run mris_compute_layer_fractions I believe (and mris_compute_layer_intensities if you want to account for partial volume effects) cheers Bruce On Thu, 2 Jul 2015, Yun Wang wrote: Hi All, I am trying to segment gray matters (anatomical) into 5 layers and then extracting different layers’ functional MRI data. I have got 5 surfaces using mir_expand function and finish the registration of fMRI to anatomical data. I want to make 5 masks and then extract the time series, does anyone know how to make ROI using surface? Thanks! Yun Wang ___ 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.
Re: [Freesurfer] correction for field dishomogeneity
I did it. Thank you very much. C Il giorno 03/lug/2015 18:51, Bruce Fischl fis...@nmr.mgh.harvard.edu ha scritto: not sure. Did you use recon-all? If so, then you did use the appropriate pipeline provided by freesurfer On Fri, 3 Jul 2015, clelia pellicano wrote: Hi Bruce, thank you for your reply. Do you have any idea about what they could mean saying without using the appropriate pipeline provided by freesurfer? Thanks BW C Il giorno 03/lug/2015 15:32, Bruce Fischl fis...@nmr.mgh.harvard.edu ha scritto: Hi Clelia yes, we correct for field inhomogeneity. Presumably they mean the B1 receive field, which is what is typically meant in structurals. If they mean B0, we don't typically correct (nor do most people for structural imaging - this is more of an issue for diffusion and functional MRI). cheers Bruce On Fri, 3 Jul 2015, clelia pellicano wrote: Dear experts, I was wondering how freesurfer corrects for field dishomogeneity. As long as I know, it's automatically done by the software . My concern is because a reviewer has made this comment (please find it below): Authors used an old 3 T MRI without using the appropriate pipeline provided by freesurfer to correct for field dysomogeneity We have run the standard pipeline provided to derive measures of cortical thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ). Here the MRI protocol used: All participants were scanned on a 3-Tesla Philips Intera whole-body MRI scanner. A T1-weighted three-dimensional magnetization-prepared rapid acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition: 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired. Any clue about? Thank you in advance. BW Clelia . Clelia Pellicano, MDPhD Student in Clinical and Experimental Neurosciences and Psychiatry, Department of Neuroscience, Mental Health and Sensory Organs, NESMOS, Sapienza University Via di Grottarossa 1035, 00189 Rome, Italy phone +390633775579 fax +390633775900 Research Neurologist Department of Clinical and Experimental Neurology Santa Lucia Foundation IRCSS Via Ardeatina 306, 00179, Rome, Italy ___ 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.
Re: [Freesurfer] correction for field dishomogeneity
not sure. Did you use recon-all? If so, then you did use the appropriate pipeline provided by freesurfer On Fri, 3 Jul 2015, clelia pellicano wrote: Hi Bruce, thank you for your reply. Do you have any idea about what they could mean saying without using the appropriate pipeline provided by freesurfer? Thanks BW C Il giorno 03/lug/2015 15:32, Bruce Fischl fis...@nmr.mgh.harvard.edu ha scritto: Hi Clelia yes, we correct for field inhomogeneity. Presumably they mean the B1 receive field, which is what is typically meant in structurals. If they mean B0, we don't typically correct (nor do most people for structural imaging - this is more of an issue for diffusion and functional MRI). cheers Bruce On Fri, 3 Jul 2015, clelia pellicano wrote: Dear experts, I was wondering how freesurfer corrects for field dishomogeneity. As long as I know, it's automatically done by the software . My concern is because a reviewer has made this comment (please find it below): Authors used an old 3 T MRI without using the appropriate pipeline provided by freesurfer to correct for field dysomogeneity We have run the standard pipeline provided to derive measures of cortical thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ). Here the MRI protocol used: All participants were scanned on a 3-Tesla Philips Intera whole-body MRI scanner. A T1-weighted three-dimensional magnetization-prepared rapid acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition: 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired. Any clue about? Thank you in advance. BW Clelia . Clelia Pellicano, MDPhD Student in Clinical and Experimental Neurosciences and Psychiatry, Department of Neuroscience, Mental Health and Sensory Organs, NESMOS, Sapienza University Via di Grottarossa 1035, 00189 Rome, Italy phone +390633775579 fax +390633775900 Research Neurologist Department of Clinical and Experimental Neurology Santa Lucia Foundation IRCSS Via Ardeatina 306, 00179, Rome, Italy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion
Basically, I try to create the .mgh files from sig.nii.gz and ces.nii.gz files needed for mri_segstats in ROI-analysis. I run already preprocessing and selxavg3-sess stats to produce the different stats files (sii/ces.nii.gz) The .mgh files show the correct anatomy-space dimension (mri_info: 1x1x1 mm; 256^3, beforehand surface dimension 141526 x 1 x 1) but seem to be corrupted. I tried to visualize the whole hemisphere sig.nii.gz converted into sig.mgh but now activations show up despite of highly significant activations visible in the sig.nii.gz To create .mgh files and run the ROI-analysis, I used the following commands: ### resample ces.nii volume to anatomical space #1 resample ces.nii.gz to anatomy mri_vol2vol --mov $sub/bold/EX.sm5.lh/EX/ces.nii.gz --reg $sub/bold/001/register.dof6.dat --fstarg --interp nearest -- o $sub/bold/EX.sm5.lh/EX/ces.lh.mgh #2 resample sig.nii.gz to anatomy mri_vol2vol --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/001/register.dof6.dat --fstarg --interp nearest --o $sub/bold/EX.sm5.lh/EX/sig.lh.mgh #3 run ROI with an unsigned functional constraint mri-segstats --seg $SUBJECTS_DIR/$sub/mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --id 410 -id 407 --i $sub/bold/EX.sm5.lh/EX/ces.lh.mgh --maskthresh 2 --masksign abs The ROI analysis always ends up with zero hrf-amplitudes. I appreciate your support, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Donnerstag, 2. Juli 2015 17:18 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion Sorry, can you backup and tell me what you are trying to accomplish? doug On 07/02/2015 10:05 AM, Milde, Christopher wrote: Dear Doug, thanks for the immediate response. Actually I checked the registration with freeview/tkregister2 and print out the quality values which are perfectly fine I did the following fMRI-analysis steps FSFAST 1. Preproc-sess (for smoothwm as well as fsaverage space) -- register.dof6.dat in bold/001 and bold/002 folders 2. Selxavg-sess on created design matrices and contrasts (one of the 1st-level stat files is called EX.sm5.lh) 3. And interrogated the results with mris_surfcluster (EX.sm5.lh/EX/ includes the sig.nii ces.nii as well as txt.files with the mris_surfcluster output) The main problem is the creation of .mgh files as inputs used for ROI-analysis in the mri_segstats cmd. So the conversion of the sig.nii ces.nii into sig.mgh and ces.mgh (using mri_vol2vol) https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriInd ividual_freeview How to transfer the surface nii.gz files into .mgh files used in volume space? Thanks, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Donnerstag, 2. Juli 2015 14:49 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion How did you create the EX.sm5.lh analysis? It is probably the case that it is already on the surface in which case you don't need to run vol2surf. doug On 07/02/2015 04:54 AM, Milde, Christopher wrote: Dear Freesurfers, I have problems converting .nii.gz files into .mgh files needed e.g. for performing ROI analysis. I used mri_vol2surf and mri_vol2vol to produce .mgh files either to visualize contrast estimates and significance maps on volumes or surfaces I think the problem is due to voxel resolution mismatches between source and registration files but I don't know how to solve this problem. I worked with different registration files: the register.dof6.dat (originally outpu from the preproc-sess) as well as register.dat and register.lta by running bbregister for the template.nii.gz - - - here is an example command: # resample to surface mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz srcreg = PM_04001/bold/register.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume regio_read_register: loading lta reading extra input line subject PM_04001 reading extra input line fscale 0.15 WARNING: the voxel resolution in the source volume (1,1,1) differs from that
Re: [Freesurfer] Help with V6
Hi Noah, this error is pretty weird. Can you please send us the exact command you executed? Regarding the runtime: your 2014b runtime won't work. You need to follow the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, July 3, 2015 4:20:02 AM Subject: [Freesurfer] Help with V6 Hi, I’m trying to run the ‘beta’ version of FS6, centos4, and encountered the error: ‘ERROR: Flag -hippocampal-subfields-T1 unrecognized’. I setenv and source just as described for previous versions. Also, I have Matlab 2014b downloaded on the computer (obviously comes with runtime) but am unsure if the runtime folder needs to be placed in the FS folder or is fine where it is. Any FS experts help with these two problems and concerns? Much appreciated if you do. Cheers, Noah Markowitz ___ 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] correction for field dishomogeneity
Dear experts, I was wondering how freesurfer corrects for field dishomogeneity. As long as I know, it's automatically done by the software . My concern is because a reviewer has made this comment (please find it below): Authors used an old 3 T MRI without using the appropriate pipeline provided by freesurfer to correct for field dysomogeneity We have run the standard pipeline provided to derive measures of cortical thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ). Here the MRI protocol used: All participants were scanned on a 3-Tesla Philips Intera whole-body MRI scanner. A T1-weighted three-dimensional magnetization-prepared rapid acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition: 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired. Any clue about? Thank you in advance. BW Clelia . Clelia Pellicano, MD PhD Student in Clinical and Experimental Neurosciences and Psychiatry, Department of Neuroscience, Mental Health and Sensory Organs, NESMOS, Sapienza University Via di Grottarossa 1035, 00189 Rome, Italy phone +390633775579 fax +390633775900 Research Neurologist Department of Clinical and Experimental Neurology Santa Lucia Foundation IRCSS Via Ardeatina 306, 00179, Rome, Italy ___ 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] Reasons for problems with resampling issues
Dear Douglas thanks a lot for your advice. I tried it, but only one volume of the stack was read. I tried to use the --frame option, but it does not work. How can I force mri_segstats with the --frame option so that all 53 volumes of the stack are read? Thanks in advance Regards Jürgen Am 02.07.15 14:44 schrieb Douglas N Greve unter freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu: There are inevitable issues around the boundaries of the cluster. For small clusters, this can be a big deal. I would probably just use the fsaverage clusters on the control group after they have been mapped to fsaverage space (ie, run mris_preproc on the control group to get a stack, smooth it, then run mri_segstats with the stack as the input and the ocn.mgh file as the --seg. doug On 07/02/2015 03:21 AM, Jürgen Hänggi wrote: Dear FS experts in a former email http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg23322.htm l it has been recommended that we should not map clusters found in an analysis in the standard space back to the individual space due to resampling issues. In one of our study, we computed a correlation across patients and controlls and get MC simulation corrected clusters, the individual values of it can be found in the .y.ocn.dat file. A reviewer suggested to do the correlation only across the patient group and then transform these clusters into the native space in order to extract the values within these clusters for the control group. Therefore we would like to know the exact reason why this resampling is not recommended. Is it related to the fact that the transform from the native to the standard space is not one-to-one? What you recommend to answer to this reviewer point? Thanks in advance Best regards Jürgen Hänggi - -- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. - -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
