[Freesurfer] Create a surface overlay with statistic results using AAL ROI
Hi all, I have some statistical results for AAL 90 coordinates (correlation coefficients from network measurements x clinical data). I would like to create an overlay to visualize in FreeSurfer standard (fsaverage) space, showing the areas with positive and negative correlations (and the scale / power of correlation, i.e. beta-value, for each area). Is it possible using FreeSurfer tools? If it is possible, how should I produce a .txt file to be read in FreeSurfer. Kind regards, Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] qdec
Hello FS experts, I am trying to run qdec. When I load my data table it appears the following error message: Loading data table /Users/carolinamrimkus/Documents/Cross_sectional_RRMS_RM1.dat... Number of columns: 290 fsid column: 1 Number of factors: 289 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. Why it is saying that I have "0" subjects if my fsid columm has 59 subjects? Thank you in advance, Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] QDEC longitudinal analysis
Hello Freesurfers, I am trying to run QDEC for a longitudinal analysis. I've run the command "long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat" to adjust my qdec table to the right format for QDEC (with only one line / subject). I've also created the .Qdecrc file in my qdec directory. But, my end up table contains the fsid with my base images. When I run the analysis, appears an error message: Error in analyze: Couldn't open /baseID/surf/lh.thickness.fwhm10.fsaverage.mgz file. Indeed, this file does not exist in the base directory (but I think it was not supposed to be there). Additionaly, I was interested in test the correlation between spc and rate and the changes in the clinical parameters of my sample. I though it would be feasible after creating .Qdecrc file. Is that right? Kind regards, Carolina ___ 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 post processing
Hello, I am trying to make the Two Stage Longitudinal processing and when I give the command to prepare the data with QCACHE. I've already set up the environment for FREESURFER_HOME, but it keeps appearing the error message: ERROR: FREESURFER_HOME not defined in environment ERROR 1 : mri_label2label mapping the label failed? Following, there is a copy of my command and the error messages that appeared. sudo long_mris_slopes --qdec $SUBJECTS_DIR/qdec/longRRMSP01.qdec.table.dat --meas thickness --hemi lh \ --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label \ --time years --qcache $SUBJECTS_DIR/fsaverage/ --sd $SUBJECTS_DIR/ Password: Parsing the qdec table: /analise//qdec/longRRMSP01.qdec.table.dat Working in SUBJECTS_DIR: /analise// Working on hemi: lh Subject-Template: P01_TP INFO: 2 TPs in P01_TP , mean age: 2.25 === SUBJECT P01_TP Intersecting Within-Subject Cortex Label cp /analise//P01_RM1.long.P01_TP/label/lh.cortex.label /analise//P01_TP/label/lh.long.cortex.label mris_label_calc intersect /analise//P01_RM2.long.P01_TP/label/lh.cortex.label /analise//P01_TP/label/lh.long.cortex.label /analise//P01_TP/label/lh.long.cortex.label === SUBJECT P01_TP mapping label to QCache mri_label2label --srclabel /analise//P01_TP/label/lh.long.cortex.label --srcsubject P01_TP --trglabel /analise//P01_TP/label/lh.long.cortex./analise//fsaverage/.label --trgsubject /analise//fsaverage/ --regmethod surface --hemi lh srclabel = /analise//P01_TP/label/lh.long.cortex.label srcsubject = P01_TP trgsubject = /analise//fsaverage/ trglabel = /analise//P01_TP/label/lh.long.cortex./analise//fsaverage/.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 ERROR: FREESURFER_HOME not defined in environment ERROR 1 : mri_label2label mapping the label failed? Thank you, Carolina ___ 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] long_mris_slopes error
Hi FreeSurfer experts, I am trying to run Longitudinal Two Steps analysis. In the long_mris_slopes I run the following command: long_mris_slopes --qdec $SUBJECTS_DIR/qdec/longRRMSP01.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/ And, after some processing, it appears the error message: mv ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp.mgh /analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh mv: rename ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp.mgh to /analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh: No such file or directory ERROR 1 : mv ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp.mgh /analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh did not work? In the base folder, /surf, I can find many .mgh archives, for example: lh.long.thickness-spc.fwhm0.mgh (and others with other fwhm smoothing factors). But I can't find any lh.long.thicknessfsaverage files. I did all the previous processing as it appears in the Longitudinal FS Tutorials. I also tried to run qcache with the base file, but it says it is not necessary, since it is a base file. Should I run qcache first with each subject / time point before? Thank you, Carolina ___ 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] Mac OS X update
Hi all, I have a simple doubt: I am updating my MAC OS X from Snow Leopard to Mavericks. I am worried if FreeSurfer is going to run perfectly in the new OS X? Thank you, Carolina ___ 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] editing segmentation
Hello, The corpus callosum (CC) segmentation in my aparc+aseg.mgz file is not OK. It has included the fornix and ventricular areas within the CC. I erased with edit tool in the tkmedit and saved the new segmentation. How do I do to reprocess the subject and correct the stats (volume, etc)? Is there a better way to correct the segmentation masks? Thank you, Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] qdec
Hello, In the qdec analysis the default smoothing factor is 10. What does it mean? For other technics such as fMRI we generally use a lower smoothing factor (~3 or lower). What would happen if I low down the FWHM? Thank you, Carolina ___ 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] Image resolution and reliability of freesurfer measurements
Hello, I would like to know if it is possible to process T1 images with a slice tickness of 5mm / 0.5mm of gap in freesurfer and obtain reliable cortical tickness measurements and parcelations? Thank you, Carolina Rimkus ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] TRACULA
Hello,Is it possible to track fibers with TRACULA from the cortical parcelation masks obtained from recon-all or do we have to use the white matter parcelation to do so?Another question: if I use QDEC to find the areas with significant difference in the cortical tickness between two groups, is it possible to use those ROI's to launch the fiber track with TRACULA?Thank you, Carolina Rimkus ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tracula
Hello,Is it possible to track fibers with TRACULA from the cortical parcelation masks obtained from recon-all or do we have to use the white matter parcelation to do so?Another question: if I use QDEC to find the areas with significant difference in the cortical tickness between two groups, is it possible to use those ROI's to launch the fiber track with TRACULA?Thank you, Carolina Rimkus ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri-convert
Hi, all,I would like to convert my DTI images from the REC-PAR format to .nii, so I could use in TRACULA and also other tools from freesurfer.Is it possible? What is the right comand line to do so?After the transformation, which image I use to register in the freesurfer domain?Thank you, Carolina ___ 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] WM hypointensities
Hello, How can I describe the method for WM hypointhensities segmentation and volume calculation? Can you suggest a reference? Thank you, Carolina ___ 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] corpus callosum segmentation
Hi,How is the segmentation of the corpus callosum is done? What are the proportions used? Are they equal in longitudinal lenth or it follows some a special segmentation?Do you know how to access the map (color map / visualization) of this segments?Thank you, Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] QDEC results and stats
Hello, all,I have 2 questions:- Does anybody know which structure is represented or correspond to "left ventral IDC" in aseg segmentation?- In QDEC analysis, when we obtatin the significant clusters and see the linear regression or correlation curve, what does it mean the "value" of the curve? Is it the regression coeficient? The level of correlation? How shall I describe it?Thank you, Carolina ___ 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] Intracranial volume
Hi, all,Does anybody know what the intracranial volume and supratentorial volume include? Does it include only the parenquima volume (white matter / gray matter volumes) or it includes the ventricules and CSF? What about the WM hhypointensities? Are they included in the WM Volume measurement or in the intracranial volume? Carolina ___ 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] volumes 2
Hi, all,One more thing about the aseg: what does the CSF volume includes (the supratentorial arachnoid space? suprat + infrat?).Thank you, Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fwd: qdec
Mensagem originalDe: carolina.mr carolina...@uol.com.br Para: freesurfer-requ...@nmr.mgh.harvard.eduAssunto: qdecEnviada: 12/08/2011 00:43 Hello, When I load my qdec table it apears an error that I don't know how to solve. It says that there is not a nemline after my last subject. Does anybody know how to solve it? The text that appears in my terminal is pasted bellow. Thank you, Carolina Reading /Applications/freesurfer/tktools/tkUtils.tcl Using /Applications/freesurfer//lib/tcl/fsgdfPlot.tcl Loading data table /analise/qdec/MS1qdec.table.dat... QdecDataTable::Load: will attempt to open as Mac text file... Number of columns: 148 fsid column: 1 Number of factors: 147 Number of subjects: 59 ERROR: QdecDataTable::Load: problem parsing file /analise/qdec/MS1qdec.table.dat This line did not appear to end with a newline: P29EX1 male 30.30 MSRR 19.01 1.04 5690.0 814 456 525 318 419 2532 1.5607 0.543 0.5892 0.8853 0.6859 0.5815 0.4185 1.5971 0.6467 0.5325 0.9628 1.1932 0.6492 0.3508 1.4455 0.5872 0.5233 0.8733 0.7933 0.6767 0.3233 1.3922 0.6489 0.4694 0.8967 1.1003 0.7251 0.2749 1.8263 0.5703 0.639 0.989 1.1874 0.5183 0.4817 1.5847 0.5872 0.5642 0.9197 0.949 0.6148 0.3852 Error loading the data table. ___ 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] freesurfer license
I have installed fressurfer and setup the environment for it, as it was described in freesurfer wikki. But I can't run the freesurfer. When I try any command it says that the command is not found. Probably, it is because I couldn't copy the license text to the .license file (I couldn't find it and I don't know how to do). Could you help me? Thank you, Carolina ___ 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.
